Means and methods for regulating gene expression

ABSTRACT

The invention relates to means and methods for regulating gene expression and production of proteinaceous molecules. The invention provides a method for producing a proteinaceous molecule in a cell comprising selecting a cell for its suitability for producing the proteinaceous molecule, providing a nucleic acid encoding the proteinaceous molecule with a nucleic acid comprising a STAR (STabilizing Anti-Repression) sequence, expressing the resulting nucleic acid in the cell and collecting the proteinaceous molecule. Providing at least one STAR sequence to a nucleic acid encoding a proteinaceous molecule will enhance production (yield) of the proteinaceous molecule by a host cell, increase the proportion of host cells with acceptable expression levels, and/or increase stability of a gene expression level.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.11/012,546, filed Dec. 14, 2004, now U.S. Pat. No. 7,267,965, whichapplication is a continuation of International Patent Application No.PCT/NL03/00410, filed May 30, 2003, published in English asInternational Patent Publication No. WO 03/106674 on Dec. 24, 2003,which claims the benefit under 35 U.S.C. §119 of European PatentApplication No. EP 02077344.6, filed Jun. 14, 2002, the entirety of eachof which are hereby incorporated by reference.

STATEMENT ACCORDING TO 37 C.F.R §1.52(e)(5)—SEQUENCE LISTING SUBMITTEDON COMPACT DISC

Pursuant to 37 C.F.R. §1.52(e)(1)(iii), a compact disc containing anelectronic version of the Sequence Listing has been submittedconcomitant with this application, the contents of which are herebyincorporated by reference. The compact disc contains the file“P60555PC00 final.txt” which is 496 KB, and created on Dec. 14, 2004. Asecond compact disk is submitted and is an identical copy of the firstcompact disc (labeled, “copy 1” and “copy 2,” respectively).

TECHNICAL FIELD

The invention relates to the fields of medicine and cellular biology.More specifically, the invention relates to means and methods forregulating gene expression, and production of proteinaceous molecules.

BACKGROUND OF THE INVENTION

Polypeptide production at industrial scale currently provides manybiologically active polypeptides for a variety of uses, includingdiagnostic and therapeutic pharmaceuticals, industrial catalysts andnourishment. Polypeptides are produced in a variety of host systems,including transgenic animals and plants, microbes, and culturedmammalian cells. In most cases, the host system is modified byrecombinant DNA techniques, for instance resulting in introduction intothe host cell of a transgene which encodes a polypeptide of interest.Such a transgene typically includes elements that influence thetranscription, translation, and/or processing of the transgene'spolypeptide coding sequence. A recombinant host is then identified andisolated which has a suitable yield of a polypeptide of interest, andthe cell population of this recombinant host is increased to an extentthat it can produce the required amount of polypeptide.

The choice of the host system depends on a number of factors including:(1) the nature and intended use of a polypeptide, and (2) the cost ofproduction. For production of biopharmaceuticals, e.g., therapeuticproteins such as hormones, cytokines, and antibodies, the host system ofchoice is usually cultured mammalian cells. Considerations with respectto product use and production cost with host cells will be discussedbelow.

(1) For in vivo therapeutic use, a therapeutic protein must not onlyhave the correct biological activity to alter the course of a disease.It must also do no harm. Most therapeutic proteins are exported from thecell by the secretory pathway. Secreted proteins are modified by aseries of post-translational events, including glycosylation, disulfidebond formation, and proteolytic processing. The post-translationalmodification systems vary among different species and cell types intheir detailed mechanisms of action. As a result, the same polypeptidechain can be detectably different when it is produced in different hostcells. These differences can be analytical, such as differences inphysical properties such as molecular mass, net electrical charge,carbohydrate composition, or structure. The differences can also befunctional, affecting for instance the biological activity of theprotein itself (catalytic activity, ligand binding characteristics,etc.), and/or its in vivo properties (immunogenicity, biological halflife, biodistribution, etc.). Functional differences can, therefore,affect both function and possible side effect(s) of a therapeuticprotein. Host cell lines that produce proteins with low efficacy are notsuitable for commercial exploitation. Furthermore, host cells whichproduce modified protein that involves significant side effects in apatient should not be used. These factors are becoming increasinglyimportant considerations during selection of a host cell line forproduction of a therapeutic protein.

(2) Therapeutic protein production in host cells is an intrinsicallycostly process. Current methods for industrial production of suchproteins often perform poorly, resulting in products that areprohibitively expensive. Poor performance can be due to limitations ofprotein expression systems and host cell lines currently in use. Theselimitations mostly have a few specific causes, including (a) failure toidentify and isolate recombinant host cell lines that have suitableproductivity of proteins (poor predictability), (b) silencing, duringthe industrial production cycle, of the transgenes that encode proteins(poor stability), and (c) low or incorrect post-translational processingand secretory capacity of the host cell line. These limitations will beconsidered separately below.

(a) Conventional methods furnish only low frequencies of recombinanthost cells that have suitable yields of proteins. Identifying andisolating these rare recombinant cell lines is a laborious and expensiveprocess. The poor predictability of conventional methods means thatoften a recombinant host cell line is selected for production that hassub-optimal productivity characteristics, simply because a superiorrecombinant cell line was not identified and isolated during theselection process.

(b) Transgenes are often subject to silencing during cultivation ofrecombinant host cells. Silencing acts by suppressing transcription of atransgene. Detailed mechanisms of silencing are still not known, anddifferent conventional methods are prone to different kinds of silencingphenomena. With one phenomenon, an individual transgene is silenced byformation of transcriptionally refractory heterochromatin at thetransgenic locus. Heterochromatin formation is influenced by theposition of genomic integration of a transgene (“position effects”(Boivin and Dura, 1998)). Transgene integration occurs more or less atrandom. Since most of the genome is heterochromatin, most transgene lociare prone to silencing due to position effects.

A second transgene-silencing phenomenon can occur when two or morecopies of a transgene are integrated into a genome during constructionof a recombinant cell line. Formation of tandem transgene repeats oftenoccurs during the initial integration step. Furthermore, in order toincrease product yield, many recombinant host cell lines are engineeredafter the integration step to amplify the copy number of a transgene,which also results in tandem transgene repeats (Kaufman, 1990). Tandemrepeats and other configurations of multiple transgene copies areparticularly prone to silencing (“repeat-induced gene silencing”(Garrick et al., 1998)).

In case that a genome contains multiple copies of a transgene, the yieldcan also decline via another phenomenon than transcriptional silencing.The number of copies of the transgene can decline during cultivation ofa recombinant host cell line. The productivity of such cell lines at thetime of selection for use is correlated with a transgene copy number,and consequently as copies of a transgene are lost, the yield declines(Kaufman, 1990).

(c) Different cell types in a mammalian organism have differentcapacities for post-translational modification and secretion ofproteins. The functions of some cell types include production of largequantities of secreted proteins; examples include lymphocytes (producingimmunoglobulins), hepatocytes (producing serum proteins), andfibroblasts (producing extracellular matrix proteins). These cell typesare favorable sources for deriving host cell lines for production ofsecreted heterologous proteins. More favorable is the use of a cell linewhose progenitor organismal cell type secretes a protein or class ofproteins of interest. For example, it is particularly favorable toexpress recombinant monoclonal antibodies in lymphocytes (or host cellsderived from lymphocytes), erythropoietin in hepatocytes (or host cellsderived from hepatocytes), and blood clotting factors (e.g., Factor VIIIand van Willebrand's factor) in endothelial cells (or host cells derivedfrom endothelial cells).

The use of specific cell types (or cell lines derived therefrom) forproduction of their affiliated proteins is favorable because suchspecific cell types will carry out proper post-translationalmodifications of produced proteins. However, specific cell types oftendo not have high secretory capacities. For example, cells of the centralnervous system, such as neurons, have low intrinsic protein secretioncapacities. These cells do secrete proteins, however, includingneurotrophins. Neurotrophins regulate the fate and shape of neuronalcells during fetal and juvenile development. Moreover, they influencepatterns of neuronal degeneration and regeneration in adults (Bibel andBarde, 2000). Production of neurotrophins for therapeutic applicationshas considerable biopharmaceutical value (e.g., Axokine™, recombinantciliary neurotrophic factor from Regeneron). In order to produceheterologous neurotrophins with post-translational modifications (andhence functional properties) that match the naturally-occurringproteins, expression in host cells derived from the central nervoussystem is favorable. However, production of polypeptides such asneurotrophins in host cell lines such as those derived from neuraltissue is inefficient using conventional methods. The predictability ofidentifying high-expressor isolates from these types of cell lines isoften poor; the yield of proteins from such cell lines is generally low,and production levels are characteristically unstable.

Another drawback to a use of specific host cells for production ofaffiliated proteins is that it is usually difficult to isolate celllines with favorable biotechnological characteristics. Thesecharacteristics for instance include the mode and rate of growth, andthe ease of introduction of a transgene. Consequently, various generalhost cell lines have been established. Examples of these include CHOcells from Chinese hamster ovary (ATCC (American Type CultureCollection) CCL-61), BHK cells from baby hamster kidney (ATCC CCL-10),and Vero cells from African green monkey kidney (ATCC CCL-81). These“general purpose” host cell lines are widely used for production of anumber of heterologous proteins. A disadvantage of general purpose celllines is that the post-translational modifications of heterologousproteins produced by them often differ from the post-translationalmodifications of the naturally occurring proteins. These differences canhave functional consequences resulting in side effects, as discussedabove.

Table 1 lists a number of proteins that are currently in use or underdevelopment for biopharmaceutical applications. It also lists the tissueor cell type in which each protein is normally produced in the humanbody. These 24 proteins (or protein classes) come from a wide range ofcells and tissue, ranging from highly secretory cells (hepatocytes,endothelial cells) to cells with low secretory capacity (e.g., neuraltissue). Currently, neither general-purpose host cells nor specific hostcells have qualities that enable optimal expression of the broadspectrum of biopharmaceutically important secreted proteins.

Hence, protein production by conventional host cell lines involves a lotof disadvantages and complications, for instance with respect to yieldand post-translational modifications. There is a need in the art forimproved protein production in recombinant host cell lines.

SUMMARY OF THE INVENTION

The present invention provides a method for producing a proteinaceousmolecule in a cell comprising selecting a cell for its suitability forproducing the proteinaceous molecule, providing a nucleic acid encodingthe proteinaceous molecule with a nucleic acid comprising a STAR(STabilizing Anti-Repression) sequence, expressing the resulting nucleicacid in the cell and collecting the proteinaceous molecule.

The STAR sequence has to be operably linked to the nucleic acid encodingthe proteinaceous molecule in order to be effective. In one embodimentof the invention, one STAR element is used. Preferably however, morethan one STAR element is used. In a particularly preferred embodiment,the nucleic acid encoding the proteinaceous molecule is provided withtwo STAR sequences; one STAR sequence at the 5′ side of the codingsequence of the nucleic acid and one STAR sequence at the 3′ side of thecoding sequence of the nucleic acid.

Description of STAR Elements

New transcription regulatory elements were disclosed by the presentinventors, which are named STAR sequences (See EP 01202581.3). STARsequences are nucleic acid sequences that comprise a capacity toinfluence transcription of genes in cis. Typically, although notnecessarily, the STAR sequences do not code by themselves for afunctional protein.

A STAR sequence has a gene transcription modulating quality in at leastone type of cell. A STAR sequence is capable of enhancing genetranscription resulting in a higher yield, increasing the proportion oftransgene-comprising host cells with acceptable expression levels,and/or increasing stability of transgenes in recombinant cell lines.

In EP 01202581.3 a method of detecting, and optionally selecting, a STARsequence is provided, comprising providing a transcription system with avariety of a fragment-comprising vectors, the vectors comprising i) anelement with a gene-transcription repressing quality, and ii) a promoterdirecting transcription of a reporter gene, the method furthercomprising performing a selection step in the transcription system inorder to identify the STAR sequence. In a preferred embodiment, thefragments are located between i) the element with a gene-transcriptionrepressing quality, and ii) the promoter directing transcription of thereporter gene. RNA polymerase initiates the transcription process afterbinding to a specific sequence, called the promoter, that signals whereRNA synthesis should begin. A STAR sequence can enhance transcriptionfrom the promoter in cis, in a given cell type and/or a given promoter.

Methods disclosed in EP 01202581.3 have been used to isolate STARelements from the human genome. Isolated human STAR elements have beenplaced in DNA vectors so as to flank transgene expression units, and thevectors have subsequently been integrated into host cell genomes.Transgene expression in these recombinant host cells has been comparedto expression in similar host cells in which the expression units arenot flanked by STAR elements. The results show that STAR elements haveat least one of three consequences for production of (heterologous)proteinaceous molecule (also referred to as (heterologous) protein): (1)they increase the predictability of identifying host cell lines thatexpress a proteinaceous molecule at industrially acceptable levels; (2)they result in host cell lines with increased protein yields; and/or (3)they result in host cell lines that exhibit more stable proteinproduction during prolonged cultivation. Each of these attributes isdiscussed in more detail below:

(1) Increased predictability: Integration of transgene expression unitscan occur at random positions throughout the host cell genome. However,much of the genome is transcriptionally silent heterochromatin. When theexpression units include STAR elements flanking the transgene, theposition of integration has a reduced effect on expression. The STARelements impair the ability of adjacent heterochromatin to silence thetransgene. Consequently, the proportion of transgene-containing hostcells with acceptable expression levels is increased.

(2) Yield: The levels of protein expression in primary populations ofrecombinant host cells, directly after transgene integration, have beensurveyed. The expression level of individuals in the populations varies.However, when the transgenes are protected by STAR elements, thevariability is reduced. This reduced variability is most conspicuous inthat fewer clones are recovered that have low levels of expression.Furthermore, the populations with STAR elements commonly haveindividuals with strikingly high expression. These high-yieldingindividuals are favorable for production of proteinaceous molecules.

(3) Increased stability: STAR elements increase the stability oftransgenes in recombinant host cell lines by ensuring that thetransgenes are not transcriptionally silenced during prolongedcultivation. Comparative trials show that, under conditions in whichtransgenes that are not protected by STAR elements are progressivelysilenced (5 to 25 passages in cultivation), STAR element-protectedtransgenes continue to be expressed at high levels. This is an advantageduring industrial production of proteinaceous molecules, during whichcell cultivation continues for prolonged periods, from a few weeks tomany months.

Hence, a STAR sequence can enhance expression of a heterologousproteinaceous molecule. In addition, a STAR sequence can enhanceexpression of a naturally produced proteinaceous molecule.

Transcription can be influenced through a direct effect of the STARsequence (or the protein(s) binding to it) on the transcription of aparticular promoter. Transcription can however, also be influenced by anindirect effect, for instance because the STAR sequence affects thefunction of one or more other regulatory elements. A STAR sequence canalso comprise a stable gene transcription quality. Frequently,expression levels drop dramatically with increasing numbers of celldivisions. With the methods disclosed in EP 01202581.3 it is possible todetect and optionally select a DNA sequence that is capable of at leastin part preventing the dramatic drop in transcription levels withincreasing numbers of cell divisions. Strikingly, fragments comprising aSTAR sequence can be detected and optionally selected with a method EP01202581.3, in spite of the fact that the method does not necessarilymeasure long term stability of transcription.

A STAR sequence is suitable for enhancing the level of transcription ofa gene of interest in a host cell. If, together with a gene of interest,a STAR sequence is also introduced into host cells, more clones can bedetected that express more than a certain amount of the gene ofinterest. As used herein, such host cells are termed “host cells withacceptable expression levels.”

Furthermore, if, together with a gene of interest, a STAR sequence isalso introduced into host cells, a higher yield of producedproteinaceous molecules can be obtained, while gene expression level isalso more stable than in the absence of such STAR sequences. Preferably,a STAR sequence derived from a plant and/or vertebrate is used. Morepreferably a human STAR sequence is used.

Sequences comprising a STAR sequence can be found by using a functionalassay, as described above. However, once a collection of such sequenceshas been identified, bioinformatics can be used to find other STARsequences. Several methods are available in the art to extract sequenceidentifiers from a family of DNA sequences sharing a certain commonfeature. Such sequence identifiers can subsequently be used to identifysequences that share one or more identifiers. Sequences sharing such oneor more identifiers are likely to be a member of the same family ofsequences, i.e., are likely to share the common feature of the family.By the present inventors a large number of sequences comprising STARactivity (so-called STAR sequences) were used to obtain sequenceidentifiers (patterns) which are characteristic for sequences comprisingSTAR activity. These patterns can be used to determine whether a testsequence is likely to contain STAR activity. A method for detecting thepresence of a STAR sequence within a nucleic acid sequence of about50-5000 base pairs is thus provided, comprising determining thefrequency of occurrence in the sequence of at least one sequence patternand determining that the frequency of occurrence is representative ofthe frequency of occurrence of at least one sequence pattern in at leastone sequence comprising a STAR sequence. In principle any method issuited for determining whether a sequence pattern is representative of aSTAR sequence. Many different methods are available in the art.Preferably, the step of determining that the occurrence isrepresentative of the frequency of occurrence of at least one sequencepattern in at least one sequence comprising a STAR sequence comprises,determining that the frequency of occurrence of at least one sequencepattern significantly differs between at least one STAR sequence and atleast one control sequence. In principle any significant difference isdiscriminative for the presence of a STAR sequence. However, in aparticularly preferred embodiment, the frequency of occurrence of atleast one sequence pattern is significantly higher in at least onesequence comprising a STAR sequence compared to at least one controlsequence.

A considerable number of sequences comprising a STAR sequence have beenidentified by the present inventors. It is possible to use thesesequences to test how efficient a pattern is in discriminating between acontrol sequence and a sequence comprising a STAR sequence. Usingso-called discriminant analysis it is possible to determine on the basisof any set of STAR sequences in a species, the most optimaldiscriminative sequence patterns or combination thereof. Thus,preferably, at least one of the patterns is selected on the basis ofoptimal discrimination between at least one sequence comprising a STARsequence and a control sequence.

In a preferred embodiment, the frequency of occurrence of a sequencepattern in a test nucleic acid is compared with the frequency ofoccurrence in a sequence known to contain a STAR sequence. In this case,a pattern is considered representative for a sequence comprising a STARsequence if the frequencies of occurrence are similar. In a preferredembodiment, another criterion is used. The frequency of occurrence of apattern in a sequence comprising a STAR sequence is compared to thefrequency of occurrence of the pattern in a control sequence. Bycomparing the two frequencies it is possible to determine for eachpattern thus analyzed, whether the frequency in the sequence comprisingthe STAR sequence is significantly different from the frequency in thecontrol sequence. In this embodiment, a sequence pattern is consideredto be representative of a sequence comprising a STAR sequence, if thefrequency of occurrence of the pattern in at least one sequencecomprising a STAR sequence is significantly different from the frequencyof occurrence of the same pattern in a control sequence. By using largernumbers of sequences comprising a STAR sequence the number of patternsfor which a statistical difference can be established increases, thusenlarging the number of patterns for which the frequency of occurrenceis representative for a sequence comprising a STAR sequence. Preferably,the frequency of occurrence is representative of the frequency ofoccurrence of at least one sequence pattern in at least two sequencescomprising a STAR sequence; more preferably, in at least five sequencescomprising a STAR sequence; and, even more preferably, in at least tensequences comprising a STAR sequence. More preferably, the frequency ofoccurrence is representative of the frequency of occurrence of at leastone sequence pattern in at least 20 sequences comprising a STARsequence. In a particularly preferred embodiment, the frequency ofoccurrence is representative of the frequency of occurrence of at leastone sequence pattern in at least 50 sequences comprising a STAR.

The patterns that are indicative for a sequence comprising a STARsequence are also dependent on the type of control nucleic acid used.The type of control sequence used is preferably selected on the basis ofthe sequence in which the presence of a STAR sequence is to be detected.In a preferred embodiment, the control sequence comprises a randomsequence comprising a similar AT/CG content as at least one sequencecomprising a STAR sequence. In another preferred embodiment, the controlsequence is derived from the same species as the sequence comprising theSTAR sequence. For instance, if a test sequence is scrutinized for thepresence of a STAR sequence, active in a plant cell, then preferably thecontrol sequence is also derived from a plant cell. Similarly, fortesting for STAR activity in a human cell, the control nucleic acid ispreferably also derived from a human genome. In a preferred embodiment,the control sequence comprises between 50% and 150% of the bases of atleast one sequence comprising a STAR sequence. In a particularlypreferred embodiment, the control sequence comprises between 90% and110% of the bases of at least one sequence comprising a STAR sequence.More preferably, between 95% and 105%.

A pattern can comprise any number of bases larger than two. Preferably,at least one sequence pattern comprises at least five, more preferablyat least six, bases. In another embodiment, at least one sequencepattern comprises at least eight bases. In a preferred embodiment, theat least one sequence pattern comprises a pattern listed in Table 6and/or Table 7. A pattern may consist of a consecutive list of bases.However, the pattern may also comprise bases that are interrupted one ormore times by a number of bases that are not or only partlydiscriminative. A partly discriminative base is, for instance, indicatedas a purine.

Preferably, the presence of STAR activity is verified using a functionalassay. Several methods are presented herein to determine whether asequence comprises STAR activity. STAR activity is confirmed if thesequence is capable of performing at least one of the followingfunctions: (i) at least in part inhibiting the effect of sequencecomprising a gene transcription repressing element of the invention,(ii) at least in part blocking chromatin-associated repression, (iii) atleast in part blocking activity of an enhancer, (iv) conferring upon anoperably linked nucleic acid encoding a transcription unit compared tothe same nucleic acid alone, (iv-a) a higher predictability oftranscription, (iv-b) a higher transcription, and/or (iv-c) a higherstability of transcription over time.

The large number of sequences comprising STAR activity identified by thepresent inventors open up a wide variety of possibilities to generateand identify sequences comprising the same activity in kind notnecessarily in amount. For instance, it is well within the reach of askilled person to alter the sequences identified in the presentinvention and test the altered sequence for STAR activity. Such alteredsequences are, therefore, also part of the present invention. Alterationcan include deletion, insertion and mutation of one or more bases in thesequences.

Sequences comprising STAR activity were identified in stretches of 400bases. However, it is expected that not all of these 400 bases arerequired to retain STAR activity. Methods to delimit the sequences thatconfer a certain property to a fragment of between 400 and 5000 basesare well known. The minimal sequence length of a fragment comprisingSTAR activity is estimated to be about 50 bases.

Table 6 (SEQ ID NOS:177-342) and Table 7 (SEQ ID NOS:343-1072) listpatterns of six bases that have been found to be over represented innucleic acid molecules comprising STAR activity. This overrepresentation is considered to be representative for a STAR sequence.The tables were generated for a family of 65 STAR sequences (SEQ IDNOS:1-65). Similar tables can be generated starting from a different setof STAR sequences, or from a smaller or larger set of STAR sequences. Apattern is representative for a STAR sequence if it is over representedin the STAR sequence compared to a sequence not comprising a STARelement. This can be a random sequence. However, to exclude a nonrelevant bias, the sequence comprising a STAR sequence is preferablycompared to a genome or a significant part thereof. Preferably, a genomeof a vertebrate or plant, more preferably, a human genome. A significantpart of a genome is, for instance, a chromosome. Preferably the sequencecomprising a STAR sequence and the control sequence are derived fromnucleic acid of the same species.

The more STAR sequences are used for the determination of the frequencyof occurrence of sequence patterns, the more representative for STARsthe patterns are that are over- or under-represented. Considering thatmany of the functional features that can be expressed by nucleic acidsare mediated by proteinaceous molecules binding to them, it is preferredthat the representative pattern is over-represented in the STARsequences. Such over-represented pattern can be part of a binding sitefor such a proteinaceous molecule. Preferably, the frequency ofoccurrence is representative of the frequency of occurrence of at leastone sequence pattern in at least two sequences comprising a STARsequence; more preferably, in at least five sequences comprising a STARsequence; and, even more preferably, in at least ten sequencescomprising a STAR sequence. More preferably, the frequency of occurrenceis representative of the frequency of occurrence of at least onesequence pattern in at least 20 sequences comprising a STAR sequence. Ina particularly preferred embodiment, the frequency of occurrence isrepresentative of the frequency of occurrence of at least one sequencepattern in at least 50 sequences comprising a STAR. Preferably, thesequences comprising a STAR sequence comprises at least one of thesequences depicted in the sequences comprising STAR1-STAR65 (SEQ IDNOS:1-65), sequences comprising STAR66 and testing set (SEQ IDNOS:66-84), and sequences comprising Arabidopsis STAR A1-A35 (SEQ IDNOS:85-119) (hereinafter SEQ ID NOS:1-119).

STAR activity is a feature shared by the sequences listed in SEQ IDNOS:1-119. However, this does not mean that they must all share the sameidentifier sequence. It is very well possible that different identifiersexist. Identifiers may confer this common feature onto a fragmentcontaining it, though this is not necessarily so.

By using more sequences comprising STAR activity for determining thefrequency of occurrence of a sequence pattern or patterns, it ispossible to select patterns that are more often than others present orabsent in such a STAR sequence. In this way it is possible to findpatterns that are very frequently over- or under-represented in STARsequences. Frequently, over- or under-represented patterns are morelikely to identify candidate STAR sequences in test sets. Another way ofusing a set of over- or under-represented patterns is to determine whichpattern or combination of patterns is best suited to identify a STAR ina sequence. Using so-called discriminative statistics, we haveidentified a set of patterns that performs best in identifying asequence comprising a STAR element. In a preferred embodiment, at leastone of the sequence patterns for detecting a STAR sequence comprises asequence pattern GGACCC (SEQ ID NO:464), CCCTGC (SEQ ID NO:816), AAGCCC(SEQ ID NO:270), CCCCCA (SEQ ID NO:298) and/or AGCACC (SEQ ID NO:336).In another embodiment, at least one of the sequence patterns fordetecting a STAR sequence comprises a sequence pattern CCCN{16}AGC (SEQID NO:415), GGCN{9}GAC (SEQ ID NO:536), CACN{13}AGG (SEQ ID NO:761),and/or CTGN{4}GCC (SEQ ID NO:839).

A list of STAR sequences can also be used to determine one or moreconsensus sequences therein. The invention, therefore, also provides aconsensus sequence for a STAR element. This consensus sequence can ofcourse be used to identify candidate STAR elements in a test sequence.

Moreover, once a sequence comprising a STAR element has been identifiedin a vertebrate it can be used by means of sequence homology to identifysequences comprising a STAR element in other species belonging tovertebrate. Preferably a mammalian STAR sequence is used to screen forSTAR sequences in other mammalian species. Similarly, once a STARsequence has been identified in a plant species, it can be used toscreen for homologous sequences with similar function in other plantspecies. The invention in one aspect provides a STAR sequence obtainableby a method according to the invention. Further provided is a collectionof STAR sequences. Preferably, the STAR sequence is a vertebrate orplant STAR sequence. More preferably, the STAR sequence is a mammalianSTAR sequence or an angiosperm (monocot, such as rice or dicot, such asArabidopsis). More preferably, the STAR sequence is a primate and/orhuman STAR sequence.

A list of sequences comprising STAR activity can be used to determinewhether a test sequence comprises a STAR element. There are, asmentioned above, many different methods for using such a list for thispurpose. In a preferred embodiment, the invention provides a method fordetermining whether a nucleic acid sequence of about 50-5000 base pairscomprises a STAR sequence, the method comprising: generating a firsttable of sequence patterns comprising the frequency of occurrence of thepatterns in a collection of STAR sequences of the invention; generatinga second table of the patterns comprising the frequency of occurrence ofthe patterns in at least one reference sequence; selecting at least onepattern of which the frequency of occurrence differs between the twotables; determining, within the nucleic acid sequence of about 50-5000base pairs, the frequency of occurrence of at least one of the selectedpatterns; and determining whether the occurrence in the test nucleicacid is representative of the occurrence of the selected pattern in thecollection of STAR sequences. Alternatively, determining comprisesdetermining whether the frequency of occurrence in the test nucleic acidis representative of the frequency occurrence of the selected pattern inthe collection of STAR sequences. Preferably, the method furthercomprises determining whether the candidate STAR comprises a genetranscription modulating quality using a method of the invention.Preferably, the collection of STARS comprises sequence as depicted inSEQ ID NOS:1-119. In another aspect, the invention provides an isolatedand/or recombinant nucleic acid sequence comprising a STAR sequenceobtainable by a method of the invention.

As mentioned above, a STAR sequence can exert its activity in adirectional way, i.e., more to one side of the fragment containing itthan to the other. Moreover, STAR activity can be amplified in amount bymultiplying the number of STAR elements. The latter suggests that a STARelement may comprise one or more elements comprising STAR activity.Another way of identifying a sequence capable of conferring STARactivity on a fragment containing it comprises selecting from avertebrate or plant sequence, a sequence comprising STAR activity andidentifying whether the selected sequence and sequences flanking theselected sequence are conserved in another species. Such conservedflanking sequences are likely to be functional sequences. In one aspect,the invention, therefore, provides a method for identifying a sequencecomprising a STAR element comprising selecting a sequence of about 50 to5000 base pairs from a vertebrate or plant species comprising a STARelement and identifying whether sequences flanking the selected sequencein the species are conserved in at least one other species. Theinvention, therefore, further provides a method for detecting thepresence of a STAR sequence within a nucleic acid sequence of about50-5000 base pairs, comprising identifying a sequence comprising a STARsequence in a part of a chromosome of a cell of a species and detectingsignificant homology between the sequence and a sequence of a chromosomeof a different species. Preferably, the species comprises a plant orvertebrate species, ideally a mammalian species. The invention alsoprovides a method for detecting the presence of a STAR element within anucleic acid sequence of about 50-5000 base pairs of a vertebrate orplant species, comprising identifying whether a flanking sequence of thenucleic acid sequence is conserved in at least one other species.

It is important to note that methods of the invention for detecting thepresence of a sequence comprising a STAR sequence using bioinformaticalinformation are iterative in nature. The more sequences comprising aSTAR sequence are identified with a method of the invention, the morepatterns are found to be discriminative between a sequence comprising aSTAR sequence and a control sequence. Using these newly founddiscriminative patterns, more sequences comprising a STAR sequence canbe identified, which, in turn, enlarges the set of patterns that candiscriminate and so on. This iterative aspect is an important aspect ofmethods provided in the present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagram illustrating the pSelect plasmid used for isolatingSTAR elements. The zeocin resistance gene is under control of the SV40promoter, and is upstream of the SV40 polyadenylation site. Upstream ofthe SV40 promoter is a tandem array of lexA operator sites. Between thelexA operators and the SV40 promoter is a cloning site; test DNAs (e.g.,size-fractionated genomic DNA) are cloned into the BamHI site. Theplasmid also has the hygromycin resistance gene (hygro) for selection oftransformed cells, the EBNA-1 and oriP sequences for plasmid replicationin mammalian cells, and the ampicillin resistance gene (ampR) and orisequence for propagation in Escherichia coli.

FIG. 2 is a diagram depicting the pSDH-CSP plasmid used for testing STARactivity. The Secreted Alkaline Phosphatase (SEAP) reporter gene isunder control of the CMV promoter, and the puromycin resistanceselectable marker (puro) is under control of the SV40 promoter. Flankingthese two genes are multiple cloning sites (MCSI and MCSII) into whichSTAR elements can be cloned. The plasmid also has an origin ofreplication (ori) and ampicillin resistance gene (amp^(R)) forpropagation in Escherichia coli.

FIG. 3 is a graph showing that STAR6 (SEQ ID NO:6) and STAR8 (SEQ IDNO:8) improve predictability and yield of transgene expression in U-2 OScells. Expression of luciferase from the CMV promoter by U-2 OS cellstransfected with pSDH-CMV, pSDH-CMV-STAR6, or pSDH-CMV-STAR8 wasdetermined. The STAR-containing constructs confer greater predictabilityand elevated yield relative to the pSDH-CMV construct alone.

FIG. 4 is a graph illustrating that STAR6 (SEQ ID NO:6), but not STAR8(SEQ ID NO:8), improves predictability and yield of transgene expressionin CHO cells. Expression of SEAP from the CMV promoter by CHO cellstransfected with pSDH-CSP, pSDH-CSP-STAR6, or pSDH-CSP-STAR8 wasdetermined. The STAR6-containing constructs confer greaterpredictability and elevated yield relative to the pSDH-CSP constructalone, identifying STAR6 (SEQ ID NO:6) as a promiscuous STAR element. Incontrast, the STAR8-containing constructs do not consistently increaseyield or predictability relative to the pSDH-CSP construct, suggestingthat STAR8 (SEQ ID NO:8) is a cell line-specific STAR element.

FIG. 5 is a graph depicting that STAR6 (SEQ ID NO:6) and STAR49 (SEQ IDNO:49) improve predictability and yield of transgene expression.Expression of SEAP from the CMV promoter by CHO cells transfected withpSDH-CSP, pSDH-CSP-STAR6, or pSDH-CSP-STAR49 was determined. TheSTAR-containing constructs confer greater predictability and elevatedyield relative to the pSDH-CSP construct alone.

FIG. 6 is a graph showing the minimal essential sequences of STAR10 (SEQID NO:10) and STAR27 (SEQ ID NO:27). Portions of the STAR elements wereamplified by PCR: STAR10 (SEQ ID NO:10) was amplified with primers E23(SEQ ID NO:166) and E12 (SEQ ID NO:155) to yield fragment 10A(corresponding approximately to the first 400 nucleotides of SEQ IDNO:10), E13 (SEQ ID NO:156) and E14 (SEQ ID NO:157) to yield fragment10B (corresponding approximately to the second 400 nucleotides of SEQ IDNO:10), and E15 (SEQ ID NO:158) and E16 (SEQ ID NO:159) to yieldfragment 10C (corresponding approximately to the third 400 nucleotidesof SEQ ID NO:10). STAR27 (SEQ ID NO:27) was amplified with primers E17(SEQ ID NO:160) and E18 (SEQ ID NO:161) to yield fragment 27A(corresponding approximately to the first 500 nucleotides of SEQ IDNO:27), E19 (SEQ ID NO:162) and E20 (SEQ ID NO:163) to yield fragment27B (corresponding to the second 500 nucleotides of SEQ ID NO:27), andE21 (SEQ ID NO:164) and E22 (SEQ ID NO:165) to yield fragment 27C(corresponding approximately to the third 500 nucleotides of SEQ IDNO:27). These sub-fragments were cloned into the pSelect vector. Aftertransfection into U-2 OS/Tet-Off/LexA-HP1 cells, the growth of thecultures in the presence of zeocin was monitored. Growth rates variedfrom vigorous (+++) to poor (+/−), while some cultures failed to survivezeocin treatment (−) due to absence of STAR activity in the DNA fragmenttested.

FIG. 7 is a graph illustrating the STAR element function in the contextof the SV40 promoter. pSDH-SV40 and pSDH-SV40-STAR6 were transfectedinto the human osteosarcoma U-2 OS cell line, and expression ofluciferase was assayed with or without protection from gene silencing bySTAR6 (SEQ ID NO:6) in puromycin-resistant clones.

FIG. 8 is a graph showing the STAR element function in the context ofthe Tet-Off promoter. pSDH-Tet and pSDH-Tet-STAR6 were transfected intothe human osteosarcoma U-2 OS cell line, and expression of luciferasewas assayed with or without protection from gene silencing by STAR6 (SEQID NO:6) in puromycin-resistant clones.

FIG. 9 is a schematic diagram of the orientation of STAR elements asthey are cloned in the pSelect vector (panel A), as they are cloned intopSDH vectors to preserve their native orientation (panel B), and as theyare cloned into pSDH vector in the opposite orientation (panel C).

FIG. 10 is a graph showing directionality of STAR66 (SEQ ID NO:66)function. The STAR66 (SEQ ID NO:66) element was cloned into pSDH-Tet ineither the native (STAR66 native) or the opposite orientation (STAR66opposite) and transfected into U-2 OS cells. Luciferase activity wasassayed in puromycin resistant clones.

FIG. 11 is a southern blot showing copy number-dependence of STARfunction. Southern blot of luciferase expression units inpSDH-Tet-STAR10, integrated into U-2 OS genomic DNA. Radioactiveluciferase DNA probe was used to detect the amount of transgene DNA inthe genome of each clone, which was then quantified with aphosphorimager.

FIG. 12 is a graph illustrating copy number-dependence of STAR function.The copy number of pSDH-Tet-STAR10 expression units in each clone wasdetermined by phosphorimagery and compared with the activity of theluciferase reporter enzyme expressed by each clone.

FIG. 13 is a schematic diagram and graphs depicting enhancer-blockingand enhancer assays. The luciferase expression vectors used for testingSTARs for enhancer-blocking and enhancer activity are shownschematically. The E-box binding site for the E47 enhancer protein isupstream of a cloning site for STAR elements. Downstream of the STARcloning site is the luciferase gene under control of a human alkalinephosphatase minimal promoter (mp). The histograms indicate the expectedoutcomes for the three possible experimental situations (see text).Panel A: Enhancer-blocking assay. Panel B: Enhancer assay.

FIG. 14 is a graph showing enhancer-blocking assay. Luciferaseexpression from a minimal promoter is activated by the E47/E-boxenhancer in the empty vector (vector). Insertion of enhancer-blockers(scs, HS4) or STAR elements (STAR elements 1, 2, 3, 6, 10, 11, 18, and27; SEQ ID NOS:1, 2, 3, 6, 10, 11, 18 and 27, respectively) blockluciferase activation by the E47/E-box enhancer.

FIG. 15 is a graph illustrating enhancer assay. Luciferase expressionfrom a minimal promoter is activated by the E47/E-box enhancer in theempty vector (E47). Insertion of the scs and HS4 elements or variousSTAR elements (STARs 1, 2, 3, 6, 10, 11, 18, and 27; SEQ ID NOS:1, 2, 3,6, 10, 11, 18 and 27, respectively) do not activate transcription of thereporter gene.

FIG. 16 illustrates STAR18 (SEQ ID NO:18) sequence conservation betweenmouse and human. The region of the human genome containing 497 base pairSTAR18 (SEQ ID NO:18) is shown (black boxes); the element occurs betweenthe HOXD8 and HOXD4 homeobox genes on human chromosome 2. It is alignedwith a region in mouse chromosome 2 that shares 72% sequence identity.The region of human chromosome 2 immediately to the left of STAR18 (SEQID NO:18) is also highly conserved with mouse chromosome 2 (73%identity; gray boxes); beyond these region, the identity drops below60%. The ability of these regions from human and mouse, eitherseparately or in combination, to confer growth on zeocin is indicated:−, no growth; +, moderate growth; ++, vigorous growth; +++, rapidgrowth.

FIG. 17 is a schematic diagram of bio-informatic analysis workflow. Fordetails, see text.

FIG. 18 is a schematic diagram showing the results of discriminantanalysis on classification of the training set of 65 STAR elements. STARelements that are correctly classified as STARs by Stepwise LinearDiscriminant Analysis (LDA) are shown in a Venn diagram. The variablesfor LDA were selected from frequency analysis results for hexamericoligonucleotides (“oligos”) and for dyads. The diagram indicates theconcordance of the two sets of variables in correctly classifying STARs.

FIG. 19 is a graph illustrating that U-2 OS/Tet-Off/lexA-HP1 cells weretransfected with candidate Arabidopsis STAR elements and cultivated atlow doxycycline concentrations. Total RNA was isolated and subjected toRT-PCR; the bands corresponding to the zeocin and hygromycin resistancemRNAs were detected by Southern blotting and quantified with aphosphorimager. The ratio of the zeocin to hygromycin signals is shownfor transfectants containing zeocin expression units flanked by 12different Arabidopsis STAR elements, the Drosophila scs element, or noflanking element.

FIG. 20 is a schematic diagram and graph illustrating that STAR elementsimprove GFP expression in CHO cells. The ppGIZ and ppGIZ-STAR7 plasmidsused for testing STAR activity are shown. The expression unit comprises(from 5′ to 3′) a transgene (encoding for the GFP protein), an IRES, anda selectable marker (zeo, conferring zeocin resistance) under control ofthe CMV promoter. The expression unit has the SV40 transcriptionalterminator at its 3′ end (t). The entire cassette with the expressionunit is either flanked by STAR7 (SEQ ID NO:7) elements (STAR7-shielded)or not (Control). The constructs are transfected to CHO-K1 cells. Stablecolonies are expanded and the GFP signal is determined on a XL-MCLBeckman Coulter flow cytometer. For each independent colony the mean ofthe GFP signal is plotted. This is taken as measure for the level of GFPexpression. The results in FIG. 20 show that in CHO cells theSTAR7-shielded construct confers greater predictability and elevated GFPexpression relative to the ppGIZ control construct alone.

FIG. 21 is a schematic diagram and graph showing that STAR elementsimprove GFP expression in NSO cells. The ppGIZ and ppGIZ-STAR7 plasmidsused for testing STAR activity are shown as in FIG. 20. The constructsare transfected to NSO cells. Stable colonies are expanded and the GFPsignal is determined on a XL-MCL Beckman Coulter flow cytometer. Foreach independent colony the mean of the GFP signal is plotted. This istaken as measure for the level of GFP expression. The results in FIG. 21show that in NSO cells the STAR7-shielded (SEQ ID NO:7) constructconfers greater predictability and elevated GFP expression relative tothe ppGIZ control construct alone.

FIG. 22 is a schematic diagram and graph depicting that STAR elementsimprove GFP expression in 293 cells. The ppGIZ and ppGIZ-STAR7 plasmidsused for testing STAR activity are shown as in FIG. 20. The constructsare transfected to 293 cells. Stable colonies are expanded and the GFPsignal is determined on a XL-MCL Beckman Coulter flow cytometer. Foreach independent colony, the mean of the GFP signal is plotted. This istaken as measure for the level of GFP expression. The results in FIG. 22show that in 293 cells the STAR7-shielded (SEQ ID NO:7) constructconfers greater predictability and elevated GFP expression relative tothe ppGIZ control construct alone.

DETAILED DESCRIPTION OF THE INVENTION Definitions

Quality

The term “quality” in relation to a sequence refers to an activity ofthe sequence.

STAR and STAR Sequence

The terms “STAR,” “STAR sequence” or “STAR element,” as used herein,refer to a DNA sequence comprising one or more of the mentioned genetranscription modulating qualities.

DNA Sequence

The term “DNA sequence” as used herein, unless otherwise specified, doesnot refer to a listing of specific ordering of bases, but rather to aphysical piece of DNA. A transcription quality with reference to a DNAsequence refers to an effect that the DNA sequence has on transcriptionof a gene of interest. “Quality” as used herein refers to detectableproperties or attributes of a nucleic acid or protein in a transcriptionsystem.

Proteinaceous Molecule

By a “proteinaceous molecule” is meant herein a molecule comprisingamino acids. At least a part of the amino acids are bound to each otherto form a peptide. Preferably, the proteinaceous molecule comprises apolypeptide. In this application, the term “proteinaceous molecule” alsoincludes “polypeptide.”

Essentially the Same Properties

By “essentially the same properties” is meant that the properties areessentially the same in kind, not necessarily in amount. For instance,if a proteinaceous molecule has essentially the same properties as apharmaceutically active compound, the proteinaceous molecule alsodisplays such pharmaceutical activity in kind, not necessarily inamount.

Naturally Occurring Proteinaceous Molecule of the Same Kind

By a “naturally occurring proteinaceous molecule of the same kind” ismeant a proteinaceous molecule with the same primary structure, which isnaturally produced in vivo, not influenced by human interference.Examples comprise an antibody produced in vivo by a lymphocyte anderythropoietin produced in vivo by a hepatocyte.

Host Cell, Host Cell Line

As used herein, the terms “host cell” and “host cell line” refer to acell and to homogeneous populations thereof that are capable ofexpressing a nucleic acid encoding a proteinaceous molecule.

Recombinant Host Cell, Recombinant Host Cell Line

The terms “recombinant host cell” and “recombinant host cell line” referto a host cell and to homogeneous populations thereof into which anucleic acid has been introduced.

Expression

As used herein, the term “expression” refers to production of aproteinaceous molecule, encoded by a nucleic acid. The production, forinstance, involves transcription of a DNA sequence, translation of thecorresponding mRNA sequence, and/or posttranslational modification. Incase of secreted proteins, it can also refer to the processes oftranscription, translation, and/or post-translational modification(e.g., glycosylation, disulfide bond formation, etc.), followed byexocytosis. In the case of multimeric proteins, it can include assemblyof the multimeric structure from the polypeptide monomers.

Silencing

The term “silencing” refers to diminution of a level of expression of agene or genes, including transgenes, typically over time. The expressionlevel can be diminished but still detectable, or diminished below thethreshold of detection.

Enhanced Expression

As used herein, “enhanced expression” of a gene encoding a proteinaceousmolecule, or enhanced production of a proteinaceous molecule, can eitherinvolve a higher yield of the proteinaceous molecule, a higherproportion of host cells with acceptable expression levels, and/or ahigher stability of a gene expression level.

Affiliated Proteinaceous Molecule of a Cell

By an “affiliated proteinaceous molecule of a cell” is meant aproteinaceous molecule which is naturally produced by the kind of cellin the organism from which the cell is derived.

For instance, erythropoietin is an affiliated proteinaceous molecule ofa hepatocyte, or of a hepatocyte-derived cell line. Likewise, anantibody is an affiliated proteinaceous molecule of a lymphocyte, or ofa lymphocyte-derived cell line, typically of a B-cell or a B-cellderived cell line.

Specific Host Cell Line

A “specific host cell line” is a host cell line derived from a cellwhich normally expresses a particular proteinaceous molecule (or classof proteinaceous molecules) in the organism from which the cell isderived.

Heterologous STAR Sequence

The term “heterologous STAR sequence” is herein used to define a STARsequence that is, for example, obtained from a different cell type (fromthe same species or organism) or is obtained from a different species ororganism (either from the same cell type or a different cell type)compared to the cell in which it is used.

Stable

“Stable” means that the observed transcription level is notsignificantly changed over at least 30 cell divisions. A stable qualityis useful in situations wherein expression characteristics should bepredictable over many cell divisions. Typical examples are cell linestransfected with foreign genes. Other examples are transgenic animalsand plants and gene therapies. Very often, introduced expressioncassettes function differently after increasing numbers of celldivisions or plant or animal generations. A stable quality preferablycomprises a capacity to maintain gene transcription in subsequentgenerations of a transgenic plant or animal. Of course, in the casewhere expression is inducible, the quality comprises the quality tomaintain inducibility of expression in subsequent generations of atransgenic plant or animal.

Acceptable Expression Level

An “acceptable expression level” means an acceptable expression levelfor commercial exploitation. Whether or not a certain expression levelis acceptable for commercial exploitation often depends on the kind ofproteinaceous molecule that is produced. Acceptable expression levels ofdifferent kinds of proteinaceous molecules often involve differentamounts of produced proteinaceous molecule.

A STAR sequence, a collection of STAR sequences, and/or a nucleic acidcomprising a STAR sequence obtainable by a method of the invention, isof course suitable for use in a method of the invention for producing aproteinaceous molecule in a cell. In one aspect, the invention,therefore, provides a method for producing a proteinaceous molecule in acell comprising selecting a cell for its suitability for producing theproteinaceous molecule, providing a nucleic acid encoding theproteinaceous molecule with a nucleic acid comprising a STAR sequence,expressing the resulting nucleic acid in the cell and collecting theproteinaceous molecule, wherein the nucleic acid comprising a STARsequence is obtainable by a method of the invention for identifying andobtaining a nucleic acid comprising a STAR sequence. The nucleic acidcomprising a STAR sequence can be identified and obtained using at leastone pattern that is representative for sequences comprising STARactivity. Preferably, the nucleic acid comprising a STAR sequence isidentified and obtained using at least one pattern as depicted in Table6 (SEQ ID NOS:177-342) or Table 7 (SEQ ID NOS:343-1072).

A cell can be selected for its suitability for producing a proteinaceousmolecule in many different ways. For instance, it can be determinedwhether the cell is competent of nucleic acid uptake. A nucleic acidencoding a proteinaceous molecule is preferably easily introduced intothe cell. Furthermore it can be determined whether the cell secretesproduced proteinaceous molecule. Secreted proteinaceous molecule canusually be easily collected. Collecting proteinaceous molecules that arenot secreted usually involves sacrificing at least part of a culture.This implicates separating a proteinaceous molecule of interest fromother cell components, optionally starting up a new culture, etc. Thisis more cumbersome. Hence, in a preferred embodiment, a method of theinvention is provided wherein the proteinaceous molecule is secreted bythe cell.

In another preferred embodiment, a method of the invention is providedwherein the cell is selected for its capability of post-translationallymodifying the proteinaceous molecule, such that the proteinaceousmolecule has essentially the same properties as a naturally occurringproteinaceous molecule of the same kind. As has been explained above,different kinds of cells display different post-translationalmodifications. As a result, the same proteinaceous molecule can bemodified differently when produced in different host cells. Thesedifferences can affect the properties of such proteinaceous molecules,such as for instance pharmaceutical properties. It is, therefore, highlypreferred to select a cell which produces a proteinaceous molecule withessentially the same properties as its naturally occurring counterpart.This does not necessarily mean that the host cell has to display exactlythe same kind of post-translational modifications, as long as theproduced proteinaceous molecule has essentially the same properties. Aproteinaceous molecule can be produced that is physically different fromits natural counterpart, but which is functionally essentially the same.

In one embodiment, of the invention, however, a cell is selected for itscapability of post-translationally modifying the proteinaceous moleculein essentially the same way as the proteinaceous molecule ispost-translationally modified in nature.

In one aspect, the invention provides a method of the invention whereinthe proteinaceous molecule comprises an affiliated proteinaceousmolecule of the cell.

It is especially preferred to choose a host cell, or a cell line derivedfrom a cell, which normally produces a proteinaceous molecule ofinterest in the organism from which the cell is derived. These cells arecapable of carrying out post-translational modifications of theiraffiliated proteinaceous molecules such that the resulting proteinaceousmolecule has the same kind of properties in kind, not necessarily inamount, as a proteinaceous molecule of the same kind which is normallypresent in the organism. Such specific cells are naturally adapted forproduction of the affiliated proteinaceous molecule. Apart from otheractivities of STAR sequences it is also possible to at least partlysolve a problem of low production of proteinaceous molecules, whichoften occurs with such specific cells. Providing at least one STARsequence to a nucleic acid encoding such proteinaceous molecule willenhance production (yield) of the proteinaceous molecule by the specificcell, increase the proportion of host cells with acceptable expressionlevels, and/or increase stability of a gene expression level.

In another preferred embodiment, a method of the invention is disclosedwherein the cell is selected for suitable growth in a suspensionculture. This facilitates culturing of the cell, and collection ofproduced proteinaceous molecule, especially when the proteinaceousmolecule is secreted into the suspension. More preferably, the cell isselected for suitable growth in a serum-free culture, since serum cancontain contaminants and pathogens. Such contaminants/pathogens oftenhave to be separated from produced proteinaceous molecule. This requiresan extra step, which consumes time and chemicals, with a potential lossof produced proteinaceous molecule. Moreover, a possibility of apresence of pathogens involves a potential risk for employees. If apathogen has been present in a culture, a produced proteinaceousmolecule is not allowed to be used anymore for commercial and/or medicalapplications.

In yet another preferred embodiment, the cell is selected for thepresence of an adenovirus Early Region 1 (E1) sequence. The presence ofan adenoviral E1 sequence enhances protein production in a cell. Hence,an adenoviral E1 sequence is suitable for host cells engineered forprotein production.

The invention also provides a method for producing a proteinaceousmolecule comprising:

-   -   providing a host cell with a nucleic acid comprising a STAR        sequence;    -   selecting a cell with enhanced expression of a proteinaceous        molecule; and    -   collecting the proteinaceous molecule.

In one embodiment, the method is performed with a host cell whose genomehas not been modified by human interference. The method then results inenhanced expression of a proteinaceous molecule which is encoded by thegenome of the host cell. The proteinaceous molecule may be normallyexpressed by the host cell in the organism from which the cell isderived, but it may also normally be subject to silencing, resulting inlittle or no expression in the host cell under normal conditions.Introduction of at least one STAR sequence can at least in part inhibitsilencing of a gene of interest induced by gene-transcription repressingchromatin. Expression of a proteinaceous molecule is enhanced byintroduction of a STAR sequence.

In another embodiment, the host cell is transfected with a nucleic acidof interest. Such nucleic acid for instance, encodes a heterologousproteinaceous molecule which is not naturally encoded by the genome ofthe host cell. Introduction of a STAR sequence also enhances expressionof such heterologous proteinaceous molecule.

The STAR sequence can be introduced randomly into the genome of the hostcell, using methods known in the art (for instance calciumprecipitation, transfection with a vector comprising a nucleic acid ofinterest, use of a gene delivery vehicle, etc). If a STAR sequence isintroduced near a nucleic acid sequence encoding a proteinaceousmolecule, it is capable of enhancing expression of the proteinaceousmolecule. Cells expressing a desired proteinaceous molecule can beisolated from cultures with randomly inserted STAR sequences.

Preferably, the STAR sequence is introduced into the host cell byhomologous recombination. A nucleic acid comprising a STAR sequence canbe provided with an additional sequence. The additional sequence can bechosen such that it is at least in part homologous to a nucleic acidsequence in the host cell which is known to be present in vicinity of agene encoding a proteinaceous molecule of interest. If a nucleic acidcomprising a STAR sequence and such additional sequence is provided tothe host cell, it can be incorporated into the host cell's genome byhomologous recombination at the site with the (partly) homologousnucleic acid sequence. As a result, the STAR sequence is introduced invicinity of the gene encoding the proteinaceous molecule of interest.Expression of the proteinaceous molecule is then enhanced by theintroduced STAR sequence.

A preferred embodiment of the present invention provides a method of theinvention wherein the STAR sequence comprises a species-specific STARsequence. More preferably, the STAR sequence comprises a celltype-specific STAR sequence.

Two types of STAR elements have been identified. Promiscuous STARelements are able to function in more than one host cell line. Forexample, STAR6 (SEQ ID NO:6) increases the predictability, yield, andstability of a transgene in both the U-2 OS human osteosarcoma cell lineand in CHO (Chinese hamster ovary) cells. Other STAR elements arespecies-specific and/or cell type-specific; for example, STAR8 (SEQ IDNO:8) increases the predictability, yield, and stability of transgenesin U-2 OS cells, but not in CHO cells (see Examples 2 and 3 and FIGS. 3and 4).

If a certain type of host cell (line) is chosen for expression of aproteinaceous molecule (for instance, because it is known to possess apreferred post-translational modification system) a STAR sequence whichis naturally present in the cell can be used in a method of theinvention. Such STAR sequence is referred to as a cell type-specificSTAR sequence. A STAR sequence which is naturally present in a speciesfrom which the cell is derived can also be used. Such STAR sequence isreferred to as a species-specific STAR sequence. A species-specific STARsequence may be naturally present in the cell type, although this is notnecessary.

A known species-specific STAR sequence or cell-type specific STARsequence can be used in a method of the invention. Alternatively, a(previously unknown) species-specific STAR sequence or cell-typespecific STAR sequence can be detected and isolated by a method asdescribed by the present inventors (EP 01202581.3). The use of aspecies-specific STAR sequence or cell type-specific STAR sequence ispreferred because such sequence is especially active in the host celland is adapted to the specific circumstances within the cell. Forinstance, such cell type-specific STAR sequence may interact with aprotein which is not present in some other cell-types. In that case, thecell type-specific STAR sequence will be less capable—if at all—ofenhancing expression in cells lacking the protein. A species-specific orcell type-specific STAR element often has functional characteristicsthat are superior to promiscuous STAR elements. Furthermore, a cellline-specific STAR element can satisfy product safety or ethicalconsiderations for use of the host cell line.

A promiscuous STAR sequence is particularly useful if no tissue specificor cell-type specific STAR sequence is known. In that case a knownpromiscuous STAR sequence can be used. This saves efforts to detect andisolate a cell-type specific STAR sequence.

Several STAR sequences are listed in SEQ ID NOS:1-119. Hence, in oneaspect, a method of the invention is provided wherein the STAR sequencecomprises a sequence as depicted in SEQ ID NOS:1-119.

In a preferred embodiment, the invention provides a cell line thatcomprises at least one heterologous STAR sequence or a functionalequivalent and/or a functional fragment thereof. In an even morepreferred embodiment, the cell line is a human cell line. The inventionprovides multiple examples of STAR sequences and also methods of testingSTAR sequences and hence, a person skilled in the art is very wellcapable of obtaining a functional equivalent and/or a functionalfragment of a STAR sequence, for example by deletion or mutation. In yetanother preferred embodiment, the invention provides a non-human cellline that comprises at least one recombinant STAR sequence derived orobtained from a human cell, i.e., a human STAR sequence. It is clearthat the amount of STAR sequences may vary, for example, a cell lineaccording to the invention may comprise two, three, or four, or evenmore STAR sequences which may either be identical or different from eachother.

In one aspect, the invention provides a cell line provided with anucleic acid comprising a STAR sequence, wherein the cell line isselected for its suitability for producing a proteinaceous molecule.Preferably, a cell line of the invention comprises a vertebrate or plantcell line. A vertebrate cell line is very suitable for producing a humanproteinaceous molecule of interest, because vertebrates arephylogenetically close related.

Plant cells are for instance very suitable for vaccine production.Vaccine production in plants can be inexpensive, while the vaccine canbe easily delivered to an individual by eating the edible portion of theplant (Mercenier et al., 2001).

A cell line of the invention is particularly suitable for production ofa proteinaceous molecule of interest, because the STAR sequence canenhance expression of a gene of interest (higher yield of aproteinaceous molecule, higher proportion of host cells with acceptableexpression levels, and/or higher stability of a gene expression level).Methods for generating a cell line are known in the art and manytechniques are known to provide a cell with a nucleic acid of interest.Furthermore, many general purpose cell lines are available. Such celllines can be dedicated to production of a certain proteinaceous moleculeusing recombinant techniques. Examples of available cell lines includeCHO cells from Chinese hamster ovary and BHK cells from baby hamsterkidney (as described above).

Another embodiment of the invention provides a cell line provided with anucleic acid comprising a STAR sequence, wherein the cell line comprisesan adenovirus Early Region 1 sequence. As has been described above, anadenoviral E1 sequence enhances cellular protein production. Morepreferably a cell line of the invention is provided wherein the cellline comprises a U-2 OS osteosarcoma, CHO, 293, HuNS-1 myeloma,WERI-Rb-1 retinoblastoma, BHK, Vero, non-secreting mouse myelomaSp2/0-Ag 14, non-secreting mouse myeloma NSO, or NCI-H295R adrenal glandcarcinoma (ATCC CRL-2128) cell line.

A cell line of the invention is particularly suitable for production ofa proteinaceous molecule, because production can be enhanced by one ormore STAR sequences (higher yield of a proteinaceous molecule, higherproportion of host cells with acceptable expression levels, and/orhigher stability of a gene expression level). A cell line of theinvention can comprise promiscuous, species-specific and/or celltype-specific STAR sequences. Furthermore, a cell line of the inventioncan be used to produce a heterologous proteinaceous molecule, and/or anaffiliated proteinaceous molecule.

Hence, a use of a cell line of the invention for the production of aproteinaceous molecule is also herewith provided. Preferably, theproteinaceous molecule comprises an affiliated protein of the cell line.

Of course, a proteinaceous molecule obtainable by a method of theinvention is also provided by the present invention.

In one aspect, the invention provides a method for selecting a cellsuitable for producing a proteinaceous molecule comprising:

-   -   providing a nucleic acid encoding the proteinaceous molecule        with a nucleic acid comprising a STAR sequence;    -   expressing the resulting nucleic acid in the cell; and    -   determining whether produced proteinaceous molecule has a        desired property.

The desired property, for instance, comprises a pharmaceutical property.The property can be influenced by post translational modification(s), aconfiguration of a produced proteinaceous molecule, etc.

In yet another aspect, the invention provides a method for selecting acell suitable for producing a proteinaceous molecule comprising:

-   -   providing a host cell with a nucleic acid comprising a STAR        sequence;    -   selecting a cell with enhanced expression of a proteinaceous        molecule; and    -   determining whether the proteinaceous molecule has a desired        property.

As has been discussed above, the nucleic acid comprising a STAR sequencecan be randomly introduced into the genome of the host cell. Preferably,however, the nucleic acid sequence is introduced into the genome of thehost cell by homologous recombination.

The invention is further explained in the following examples. Theexamples do not limit the invention in any way. They merely serve toclarify the invention.

EXAMPLES Example 1 Method for Isolation of Star Elements from the HumanGenome

STAR elements are identified and cloned from human genomic DNA based ontheir ability to block the spread of transcriptional repression from DNAbinding sites for repressor proteins in a test vector, as described inthis example. The method described in this example is applicable inprinciple to any mammalian cell line, for isolation of both promiscuousand cell line-specific STAR elements.

A Method to Isolate Human Star Elements Functional in U-2 Os Cell

Materials and Methods

Plasmids and strains. The selection vector for STAR elements,pSelect-SV40-zeo (“pSelect,” FIG. 1) was constructed as follows: thepREP4 vector (Invitrogen V004-50) was used as the plasmid backbone. Itprovides the Epstein Barr oriP origin of replication and EBNA-1 nuclearantigen for high-copy episomal replication in primate cell lines; thehygromycin resistance gene with the thymidine kinase promoter andpolyadenylation site, for selection in mammalian cells; and theampicillin resistance gene and colE1 origin of replication formaintenance in Escherichia coli. The vector contains four consecutiveLexA operator sites between XbaI and NheI restriction sites (Bunker andKingston, 1994). Embedded between the LexA operators and the NheI siteis a polylinker consisting of the following restriction sites:HindIII-AscI-BamHI-AscI-HindIII. Between the NheI site and a SalI siteis the zeocin resistance gene with the SV40 promoter and polyadenylationsite, derived from pSV40/Zeo (Invitrogen V502-20); this is theselectable marker for the STAR screen.

Gene libraries were constructed by Sau3AI digestion of human genomicDNA, either purified from placenta (Clontech 6550-1) or carried inbacterial/P1 (BAC/PAC) artificial chromosomes. The BAC/PAC clonescontain genomic DNA from the 1q12 cytogenetic region (clones RP1154H19and RP3328E19), from the HOX cluster of homeotic genes (clonesRP1167F23, RP1170019, and RP11387A1), or from human chromosome 22(Research Genetics 96010-22). The DNAs were size-fractionated, and the0.5-2 kb size fraction ligated into BamHI-digested pSelect vector, bystandard techniques (Sambrook et al., 1989).

The construction of the host strains has been described (van der Vlag etal., 2000). Briefly, they are based on the U-2 OS human osteosarcomacell line (American Type Culture Collection HTB-96). U-2 OS was stablytransfected with the pTet-Off plasmid (Clontech K1620-A), encoding aprotein chimera consisting of the Tet-repressor DNA binding domain andthe VP16 transactivation domain. The cell line was subsequently stablytransfected with fusion protein genes containing the LexA DNA bindingdomain, and the coding regions of HP1, MeCP2, or HPC2 (three Drosophilaproteins that repress gene expression when tethered to DNA). TheLexA-repressor genes are under control of the Tet-Off transcriptionalregulatory system (Gossen and Bujard, 1992).

Library screening and STAR element characterization. The gene librariesin pSelect were transfected into U-2 OS/Tet-Off/LexA-repressor celllines by calcium phosphate precipitation (Graham and van der Eb, 1973,Wigler et al., 1978) as recommended by the supplier of the transfectionreagent (Life Technologies). Transfected cells were cultured underhygromycin selection (25 μg/ml) and tetracycline repression(doxycycline, 10 ng/ml) for one week (50% confluence). Then thedoxycycline concentration was reduced to 0.1 ng/ml to induce theLexA-repressor genes, and after two days zeocin was added to 250 μg/ml.The cells are cultured for a further four to five weeks, until thecontrol cultures (transfected with empty pSelect) were killed by thezeocin.

Zeocin-resistant colonies from the library transfection were propagated,and plasmid DNA isolated and rescued into E. coli by standard techniques(Sambrook et al., 1989). The candidate STAR elements in the rescued DNAwere analyzed by restriction endonuclease mapping (Sambrook et al.,1989), and tested for STAR activity (zeocin resistance) afterre-transfection to U-2 OS/Tet-Off/LexA-repressor cells and lowering thedoxycycline concentration.

The human genomic DNA inserts in these plasmids were sequenced by thedideoxy method (Sanger et al., 1977) using a Beckman CEQ™2000 automatedDNA sequencer, using the manufacturer's instructions. Briefly, DNA waspurified from E. coli using QIAprep® Spin Miniprep and Plasmid Midi Kits(QIAGEN® 27106 and 12145, respectively). Cycle sequencing was carriedout using custom oligonucleotides corresponding to the pSelect vector(primers D89 (SEQ ID NO:149) and D95 (SEQ ID NO:154); alloligonucleotides are described in Table 2), in the presence of dyeterminators (CEQ™ Dye Terminator Cycle Sequencing Kit, Beckman 608000).Assembled STAR DNA sequences were located in the human genome usingBLAST (Basic Local Alignment Search Tool (Altschul et al., 1990);worldwideweb.ncbi.nlm.nih.gov/BLAST/).

Results

The screens of human genomic DNA have yielded 66 STAR elements; thelengths and chromosomal locations of these elements are tabulated in SEQID NO:1-SEQ ID NO:66. They confer zeocin resistance on U-2 OS host cellswhen placed between LexA-repressor binding sites and the zeocinresistance gene. Their anti-repression activity was demonstrated both inthe initial screen and upon re-transfection (demonstrating that theanti-repression activity is due to the STAR element and not to somaticacquisition of zeocin resistance). The STAR elements correspond to knownand unique sequences in the human genome, as demonstrated by BLASTsearches (Table 3). In some cases, the cloned element is a chimera oftwo unlinked genomic loci (e.g., STAR3 (SEQ ID NO:3), Table 3). Theyrange in length from 500 to 2361 base pairs in length.

Example 2 Predictability and Yield is Improved by Promiscuous StarElements in More than One Host Cell Line

STAR elements function to block the effect of transcriptional repressioninfluences on transgene expression units. These repression influencescan be due to heterochromatin (“position effects”) or to adjacent copiesof the transgene (“repeat-induced gene silencing”). Two of the benefitsof STAR elements for heterologous protein production are increasedpredictability of finding high-expressing primary recombinant host cellsand increased yield during production cycles. These benefits areillustrated in this example.

Materials and Methods

Construction of the pSDH vectors and STAR-containing derivatives: ThepSDH-Tet vector was constructed by polymerase chain reactionamplification (PCR) of the luciferase open reading frame from plasmidpREP4-HSF-Luc (van der Vlag et al., 2000) using primers C67 (SEQ IDNO:136) and C68 (SEQ ID NO:137), and insertion of the SacII/BamHIfragment into SacII/BamHI-digested pUHD10-3 (Gossen and Bujard, 1992).The luciferase expression unit was re-amplified with primers C65 (SEQ IDNO:134) and C66 (SEQ ID NO:135), and re-inserted into pUHD10-3 in orderto flank it with multiple cloning sites (MCSI and MCSII). An AscI sitewas then introduced into MCSI by digestion with EcoRI and insertion of alinker (comprised of annealed oligonucleotides D93 (SEQ ID NO:152) andD94 (SEQ ID NO:153)). The CMV promoter was amplified from plasmidpCMV-Bsd (Invitrogen K510-01) with primers D90 (SEQ ID NO:150) and D91(SEQ ID NO:151), and used to replace the Tet-Off promoter in pSDH-Tet bySalI/SacII digestion and ligation to create vector pSDH-CMV. Theluciferase open reading frame in this vector was replaced by SEAP(Secreted Alkaline Phosphatase) as follows: vector pSDH-CMV was digestedwith SacII and BamHI and made blunt; the SEAP open reading frame wasisolated from pSEAP-basic (Clontech 6037-1) by EcoRI/SalI digestion,made blunt and ligated into pSDH-CMV to create vector pSDH-CS. Thepuromycin resistance gene under control of the SV40 promoter wasisolated from plasmid pBabe-Puro (Morgenstern and Land, 1990) by PCR,using primers C81 (SEQ ID NO:138) and C82 (SEQ ID NO:139). This wasligated into vector pGL3-control (BamHI site removed) (Promega E1741)digested with NcoI/XbaI to create pGL3-puro. pGL3-puro was digested withBglII/SalI to isolate the SV40-puro resistance unit, which was madeblunt and ligated into NheI digested, blunt-ended pSDH-CS. The resultingvector, pSDH-CSP, is shown in FIG. 2. All cloning steps were carried outfollowing the instructions provided by the manufacturers of the reagentsused, according to methods known in the art (Sambrook et al., 1989).

STAR elements were inserted into MCSI and MCSII in two steps, bydigestion of the STAR element and the pSDH-CSP vector with anappropriate restriction enzyme, followed by ligation. The orientation ofSTAR elements in recombinant pSDH vectors was determined by restrictionmapping, and in all cases verified by DNA sequence analysis usingprimers C85 (SEQ ID NO:140), E42 (SEQ ID NO:168), and E25 (SEQ IDNO:167) (Table 2; see Example 1).

Transfection and culture of U-2 OS cells with pSDH-CMV plasmids: Thehuman osteosarcoma U-2 OS cell line (ATCC #HTB-96) was cultured inDulbecco's Modified Eagle Medium+10% Fetal Calf Serum containingglutamine, penicillin, and streptomycin (supra) at 37° C./5% CO₂. Cellswere co-transfected with the pSDH-CMV vector and its derivativescontaining STAR6 (SEQ ID NO:6) or STAR8 (SEQ ID NO:8) in MCSI and MCSII(along with plasmid pBabe-Puro) using SuperFect® (supra). Puromycinselection was complete in two weeks, after which time individualpuromycin resistant U-2 OS/pSDH-CMV clones were isolated at random andcultured further.

Luciferase assay: Luciferase activity (Himes and Shannon, 2000) wasassayed in resuspended cells according to the instructions of the assaykit manufacturer (Roche 1669893), using a luminometer (Turner 20/20TD).Total cellular protein concentration was determined by the bicinchoninicacid method according to the manufacturer's instructions (Sigma B-9643),and used to normalize the luciferase data.

Transfection and culture of CHO cells with pSDH-CSP plasmids: TheChinese Hamster Ovary cell line CHO-K1 (ATCC CCL-61) was cultured inHAMS-F12 medium+10% Fetal Calf Serum containing 2 mM glutamine, 100 U/mlpenicillin, and 100 micrograms/ml streptomycin at 37° C./5% CO₂. Cellswere transfected with recombinant pSDH-CSP vectors using SuperFect®(QIAGEN®) as described by the manufacturer. Briefly, cells were seededto culture vessels and grown overnight to 70-90% confluence. SuperFect®reagent was combined with plasmid DNA (linearized in this example bydigestion with PvuI) at a ratio of 6 microliters per microgram (e.g.,for a 10 cm Petri dish, 20 micrograms DNA and 120 microlitersSuperFect®) and added to the cells. After overnight incubation, thetransfection mixture was replaced with fresh medium, and the transfectedcells were incubated further. After overnight cultivation, 5micrograms/ml puromycin was added. Puromycin selection was complete intwo weeks, after which time individual puromycin resistant CHO/pSDH-CSPclones were isolated at random and cultured further.

Secreted Alkaline Phosphatase (SEAP) assay: SEAP activity (Berger etal., 1988, Henthorn et al., 1988, Kain, 1997, Yang et al., 1997) in theculture medium of CHO/pSDH-CSP clones was determined as described by themanufacturer (Clontech Great EscAPe kit #K2041). Briefly, an aliquot ofmedium was heat inactivated at 65° C., then combined with assay bufferand CSPD chemiluminescent substrate and incubated at room temperaturefor ten minutes. The rate of substrate conversion was then determined ina luminometer (Turner 20/20TD). Cell density was determined by countingtrypsinized cells in a Coulter ACT10 cell counter. Luminescence unitswere converted into picograms SEAP based on a SEAP positive controlcalibration curve, and normalized to cell number.

Results

Recombinant U-2 OS cell clones containing the pSDH-CMV vector, or apSDH-CMV plasmid containing STAR6 (SEQ ID NO:6) (Table 3), were culturedfor three weeks. The luciferase activity in the host cells was thendetermined, and is expressed as relative luciferase units (FIG. 3),normalized to total cell protein. The recombinant U-2 OS clones withSTAR6 (SEQ ID NO:6) flanking the expression units had higher yields thanthe STAR-less clones: the STAR6 clones had maximal luciferase expressionlevels five-fold higher than the STAR-less clones. The STAR6 (SEQ IDNO:6) element conferred greater predictability as well: 15-20% of theclones expressed luciferase at levels comparable to or greater than theSTAR-less clone with the highest expression level.

Recombinant CHO cell clones containing the pSDH-CSP vector, or apSDH-CSP plasmid containing STAR6 (SEQ ID NO:6), were cultured for threeweeks. The SEAP activity in the culture supernatants was thendetermined, and is expressed on the basis of cell number (FIG. 4). Ascan be seen, clones with the STAR6 (SEQ ID NO:6) element in theexpression units were isolated that express two- to three-fold higherSEAP activity than clones whose expression units do not include thisSTAR element. Furthermore, the number of STAR6-containing (SEQ IDNO:6-containing) clones that express SEAP activity at or above themaximal activity of the STAR-less clones is quite high: 40% of the STAR6clone populations exceed the highest SEAP expression of the pSDH-CSPclones.

These results demonstrate that, when used with the strong CMV promoter,the STAR6 (SEQ ID NO:6) element increases the yield of this heterologousprotein in both of the host cell lines tested. STAR6 (SEQ ID NO:6) alsoconfers increased predictability, as manifested by the large proportionof the clones with yields equal to or greater than the highest yielddisplayed by the STAR-less clones. Thus, STAR6 (SEQ ID NO:6) is anexample of a promiscuous STAR element, able to suppress transgenerepression in more than one host cell line. The cell lines used arederived from different species (human and hamster) and different tissuetypes (bone and ovary), reflecting the broad range of host cells inwhich this STAR element can be utilized in improving heterologousprotein expression.

Example 3 STAR8 (SEQ ID NO:8) is a Cell Line-Specific STAR Element

The patterns of gene expression and epigenetic gene regulation in a hostcell line reflect the developmental state of the somatic cells fromwhich they are derived. Furthermore, the biotechnology industry takesadvantage of general purpose cell lines from different species accordingto specific requirements of a heterologous protein production process.Therefore, it is expected that some STAR elements will not function incell lines other than those in which they are isolated. This expectationhas been fulfilled by some of the STAR elements shown in Table 3. Oneexample will be given here.

Materials and Methods

pSDH vector construction, transfection and cultivation of CHO and U-2 OScell lines, and assay methods for the SEAP and luciferase reporter geneshas been described in Example 2.

Results

Recombinant U-2 OS cell clones containing the pSDH-CMV vector, or apSDH-CMV plasmid containing STAR8 (SEQ ID NO:8) (Table 3), were culturedfor three weeks. The luciferase activity in the host cells was thendetermined, and is expressed as relative luciferase units (FIG. 3),normalized to total cell protein. The recombinant U-2 OS clones with theSTAR8 (SEQ ID NO:8) element flanking the expression units had higheryields than the STAR-less clones: the highest expression observed fromSTAR8 clones was two- to three-fold higher than the expression fromSTAR-less clones. The STAR8 (SEQ ID NO:8) element conferred greaterpredictability as well: for this STAR element, ˜15% of the clonesdisplayed luciferase expression at levels comparable to or greater thanthe STAR-less clone with the highest expression level.

Recombinant CHO cell clones transfected with the pSDH-CSP vector, or apSDH-CSP plasmid containing STAR8 (SEQ ID NO:8), were cultured for threeweeks. The SEAP activity in the culture supernatants was thendetermined, and is expressed on the basis of cell number (FIG. 4). Ascan be seen, one clone with the STAR8 (SEQ ID NO:8) element in theexpression unit had a yield approximately two-fold higher than thehighest-expressing STAR-less clone. However, the rest of the STAR8clones expressed very poorly relative to the STAR-less clone population.Since only one individual in the STAR8 population had a good yield, itis probable that the expression unit in this clone was integrated inopen, transcriptionally active chromatin, and the high yield does notreflect anti-repression activity of STAR8 (SEQ ID NO:8) in CHO cells.Certainly in the CHO clones transfected with STAR8-containing (SEQ IDNO:8-containing) expression units the predictability is quite poor; ofthe 17 puromycin-resistant clones, only one clone had a yield of SEAPactivity above the background level of expression.

This example demonstrates that good performance of a STAR element in onecell line (in this case, the U-2 OS cell line in which STAR8 (SEQ IDNO:8) was originally isolated) is not an accurate predictor of itsperformance in other cell lines. STAR8 (SEQ ID NO:8) is thus an exampleof a cell line-specific STAR element.

Example 4 STAR Elements Functionality in Diverse Cell Line

Materials and Methods

Cell lines including the U-2 OS osteosarcoma and CHO (Chinese hamsterovary) cell lines (supra), the 293 cell line (ATCC CRL-1573) derivedfrom human embryonal kidney (immortalized by adenovirus 5 transfection),the HuNS-1 myeloma (ATCC CRL-8644) and the WERI-Rb-1 retinoblastoma cellline (ATCC HTB-169), the NCI-H295R adrenal gland carcinoma (ATCCCRL-2128), and the non-secreting mouse myelomas Sp2/0-Ag 14 and NSO areexamined according to the previous examples.

Example 5 STAR Elements Improve the Stability of Transgene Expression

During cultivation of recombinant host cells, it is common practice tomaintain antibiotic selection. This is intended to preventtranscriptional silencing of the transgene, or loss of the transgenefrom the genome by processes such as recombination. However it isundesirable for production of heterologous proteins, for a number ofreasons. First, the antibiotics that are used are quite expensive, andcontribute significantly to the unit cost of the product. Second, forbiopharmaceutical use, the protein must be demonstrably pure, with notraces of the antibiotic in the product. One advantage of STAR elementsfor heterologous protein production is that they confer stableexpression on transgenes during prolonged cultivation, even in theabsence of antibiotic selection; this property is demonstrated in thisexample.

Materials and Methods

The U-2 OS cell line was transfected with the plasmid pSDH-Tet-STAR6 andcultivated as described in Example 2. Individual puromycin-resistantclones were isolated and cultivated further in the absence ofdoxycycline. At weekly intervals the cells were transferred to freshculture vessels at a dilution of 1:20. Luciferase activity was measuredat periodic intervals as described in Example 2. After 15 weeks, thecultures were divided into two replicates; one replicate continued toreceive puromycin, while the other replicate received no antibiotic forthe remainder of the experiment (25 weeks total).

Results

Table 4 presents the data on luciferase expression by an expression unitflanked with STAR6 (SEQ ID NO:6) during prolonged growth with or withoutantibiotic. As can be seen, the expression of the reporter transgene,luciferase, remains stable in the U-2 OS host cells for the duration ofthe experiment. After the cultures were divided into two treatments(plus antibiotic and without antibiotic) the expression of luciferasewas essentially stable in the absence of antibiotic selection. Thisdemonstrates the ability of STAR elements to protect transgenes fromsilencing or loss during prolonged cultivation. It also demonstratesthat this property is independent of antibiotic selection. Therefore,production of heterologous proteins is possible without incurring thecosts of the antibiotic or of difficult downstream processing.

Example 6 Minimal Essential Sequences of STAR Elements

STAR elements are isolated from the genetic screen described inExample 1. The screen uses libraries constructed with human genomic DNAthat was size-fractionated to approximately 0.5-2 kilobases (supra). TheSTAR elements range from 500 to 2361 base pairs (Table 3). It is likelythat, for many of the STAR elements that have been isolated, STARactivity is conferred by a smaller DNA fragment than the initiallyisolated clone. It is useful to determine these minimum fragment sizesthat are essential for STAR activity, for two reasons. First, smallerfunctional STAR elements would be advantageous in the design of compactexpression vectors, since smaller vectors transfect host cells withhigher efficiency. Second, determining minimum essential STAR sequencespermits the modification of those sequences for enhanced functionality.Two STAR elements have been fine-mapped to determine their minimalessential sequences.

Materials and Methods

STAR10 (SEQ ID NO:10) (1167 base pairs) and STAR27 (SEQ ID NO:27) (1520base pairs) have been fine-mapped. They have been amplified by PCR toyield sub-fragments of approximately equal length (FIG. 6 legend). Forinitial testing, these have been cloned into the pSelect vector at theBamHI site, and transfected into U-2 OS/Tet-Off/LexA-HP1 cells asdescribed in Example 1. After selection for hygromycin resistance,LexA-HP1 was induced by lowering the doxycycline concentration.Transfected cells were then incubated with zeocin to test the ability ofthe STAR fragments to protect the SV40-Zeo expression unit fromrepression due to LexA-HP1 binding.

Results

In this experiment STAR10 (SEQ ID NO:10) and STAR 27 (SEQ ID NO:27)confer good protection against gene silencing, as expected (FIG. 6).This is manifested by robust growth in the presence of zeocin.

Of the three STAR10 (SEQ ID NO:10) sub-fragments, 10A (˜400 base pairs,corresponding to approximately the first 400 nucleotides of SEQ IDNO:10) confers on transfected cells vigorous growth in the presence ofzeocin, exceeding that of the full-length STAR element. Cellstransfected with pSelect constructs containing the other twosub-fragments do not grow in the presence of zeocin. These resultsidentify the ˜400 base pair 10A fragment as encompassing the DNAsequence responsible for the anti-repression activity of STAR10 (SEQ IDNO:10).

STAR27 (SEQ ID NO:27) confers moderate growth in zeocin to transfectedcells in this experiment (FIG. 6). One of the sub-fragments of thisSTAR, 27B (˜500 base pairs, corresponding to approximately the second500 nucleotides of SEQ ID NO:27), permits weak growth of the host cellsin zeocin-containing medium. This suggests that the anti-repressionactivity of this STAR is partially localized on sub-fragment 27B, butfull activity requires sequences from 27A (corresponding toapproximately the first 500 nucleotides of SEQ ID NO:27) and/or 27C(corresponding to approximately the third 500 nucleotides of SEQ IDNO:27) (each ˜500 base pairs) as well.

Example 7 STAR Elements Function in the Context of VariousTranscriptional Promoters

Transgene transcription is achieved by placing the transgene openreading frame under control of an exogenous promoter. The choice ofpromoter is influenced by the nature of the heterologous protein and theproduction system. In most cases, strong constitutive promoters arepreferred because of the high yields they can provide. Some viralpromoters have these properties; the promoter/enhancer of thecytomegalovirus immediate early gene (“CMV promoter”) is generallyregarded as the strongest promoter in common biotechnological use(Boshart et al., 1985, Doll et al., 1996, Foecking and Hofstetter,1986). The simian virus SV40 promoter is also moderately strong (Boshartet al., 1985, Foecking and Hofstetter, 1986) and is frequently used forectopic expression in mammalian cell vectors. The Tet-Off promoter isinducible: the promoter is repressed in the presence of tetracycline orrelated antibiotics (doxycycline is commonly used) in cell-lines whichexpress the tTA plasmid (Clontech K1620-A), and removal of theantibiotic results in transcriptional induction (Deuschle et al., 1995,Gossen and Bujard, 1992, Izumi and Gilbert, 1999, Umana et al., 1999).

Materials and Methods

The construction of the pSDH-Tet and pSDH-CMV vectors is described inExample 2. pSDH-SV40 was constructed by PCR amplification of the SV40promoter (primers D41 (SEQ ID NO:142) and D42 (SEQ ID NO:143)) fromplasmid pSelect-SV40-Zeo (Example 1), followed by digestion of the PCRproduct with SacII and SalI. The pSDH-CMV vector was digested with SacIIand SalI to remove the CMV promoter, and the vector and SV40 fragmentwere ligated together to create pSDH-SV40. STAR6 (SEQ ID NO:6) wascloned into MCSI and MCSII as described in Example 2. The plasmidspSDH-Tet, pSDH-Tet-STAR6, pSDH-Tet-STAR7, pSDH-SV40 and pSDH-SV40-STAR6were co-transfected with pBabe-Puro into U-2 OS using SuperFect® asdescribed by the manufacturer. Cell cultivation, puromycin selection,and luciferase assays were carried out as described in Example 2.

Results

FIGS. 3, 7, and 8 compare the expression of the luciferase reporter genefrom three different promoters: two strong and constitutive viralpromoters (CMV and SV40), and the inducible Tet-Off promoter. All threepromoters were tested in the context of the STAR6 (SEQ ID NO:6) elementin U-2 OS cells. The results demonstrate that the yield andpredictability from all three promoters are increased by STAR6 (SEQ IDNO:6). As described in Examples 2 and 5, STAR6 (SEQ ID NO:6) isbeneficial in the context of the CMV promoter (FIG. 3). Similarimprovements are seen in the context of the SV40 promoter (FIG. 7): theyield from the highest-expressing STAR6 clone is two- to three-foldgreater than the best pSDH-SV40 clones, and six STAR clones (20% of thepopulation) have yields higher than the best STAR-less clones. In thecontext of the Tet-Off promoter under inducing (low doxycycline)concentrations, STAR6 (SEQ ID NO:6) also improves the yield andpredictability of transgene expression (FIG. 8): the highest-expressingSTAR6 clone has a 20-fold higher yield than the best pSDH-Tet clone, andnine STAR6 clones (35% of the population) have yields higher than thebest STAR-less clone. It is concluded that this STAR element isversatile in its transgene-protecting properties, since it functions inthe context of various biotechnologically useful promoters oftranscription.

Example 8 STAR Element Function can be Directional

While short nucleic acid sequences can be symmetrical (e.g.,palindromic), longer, naturally-occurring sequences are typicallyasymmetrical. As a result, the information content of nucleic acidsequences is directional and the sequences themselves can be describedwith respect to their 5′ and 3′ ends. The directionality of nucleic acidsequence information affects the arrangement in which recombinant DNAmolecules are assembled using standard cloning techniques known in theart (Sambrook et al., 1989). STAR elements are long, asymmetrical DNAsequences, and have a directionality based on the orientation in whichthey were originally cloned in the pSelect vector. In the examples givenabove, using two STAR elements in pSDH vectors, this directionality waspreserved. This orientation is described as the native or 5′-3′orientation, relative to the zeocin resistance gene (see FIG. 9). Inthis example the importance of directionality for STAR function istested in the pSDH-Tet vector. Since the reporter genes in the pSDHvectors are flanked on both sides by copies of the STAR element ofinterest, the orientation of each STAR copy must be considered. Thisexample compares the native orientation with the opposite orientation(FIG. 9).

Materials and Methods

The STAR66 (SEQ ID NO:66) element was cloned into pSDH-Tet as describedin Example 2. U-2 OS cells were co-transfected with plasmidspSDH-Tet-STAR66-native and pSDH-Tet-STAR66-opposite, and cultivated asdescribed in Example 2. Individual clones were isolated and cultivated;the level of luciferase expression was determined as described (supra).

Results

The results of the comparison of STAR66 (SEQ ID NO:66) activity in thenative orientation and the opposite orientation are shown in FIG. 10.When STAR66 (SEQ ID NO:66) is in the opposite orientation, the yield ofonly one clone is reasonably high (60 luciferase units). In contrast,the yield of the highest-expressing clone when STAR66 (SEQ ID NO:66) isin the native orientation is considerably higher (100 luciferase units)and the predictability is much higher, as well: seven clones of thenative-orientation population (30%) express luciferase above the levelof the highest-expressing clone from the opposite-orientationpopulation, and 15 of the clones in the native-orientation population(60%) express luciferase above ten relative luciferase units. Therefore,it is demonstrated that STAR66 (SEQ ID NO:66) function is directional.

Example 9 Transgene Expression in the Context of STAR Elements is CopyNumber-Dependent

Transgene expression units for heterologous protein expression aregenerally integrated into the genome of the host cell to ensure stableretention during cell division. Integration can result in one ormultiple copies of the expression unit being inserted into the genome;multiple copies may or may not be present as tandem arrays. Theincreased yield demonstrated for transgenes protected by STAR elements(supra) suggests that STAR elements are able to permit the transgeneexpression units to function independently of influences ontranscription associated with the site of integration in the genome(independence from position effects (Boivin and Dura, 1998)). Itsuggests further that the STAR elements permit each expression unit tofunction independently of neighboring copies of the expression unit whenthey are integrated as a tandem array (independence from repeat-inducedgene silencing (Garrick et al., 1998)). Copy number-dependence isdetermined from the relationship between transgene expression levels andcopy number, as described in the example below.

Materials and Methods

U-2 OS cells were co-transfected with pSDH-Tet-STAR10 and cultivatedunder puromycin selection as described (supra). Eight individual cloneswere isolated and cultivated further. Then cells were harvested, and oneportion was assayed for luciferase activity as described (supra). Theremaining cells were lysed and the genomic DNA purified using theDNeasy® Tissue Kit (QIAGEN® 69504) as described by the manufacturer. DNAsamples were quantitated by UV spectrophotometry. Three micrograms ofeach genomic DNA sample were digested with PvuII and XhoI overnight asdescribed by the manufacturer (New England Biolabs), and resolved byagarose gel electrophoresis. DNA fragments were transferred to a nylonmembrane as described (Sambrook et al., 1989), and hybridized with aradioactively labeled probe to the luciferase gene (isolated fromBamHI/SacII-digested pSDH-Tet). The blot was washed as described(Sambrook et al., 1989) and exposed to a phosphorimager screen (PersonalF/X, BioRad). The resulting autoradiogram (FIG. 11) was analyzed bydensitometry to determine the relative strength of the luciferase DNAbands, which represents the transgene copy number.

Results

The enzyme activities and copy numbers (DNA band intensities) ofluciferase in the clones from the pSDH-Tet-STAR10 clone population isshown in FIG. 12. The transgene copy number is highly correlated withthe level of luciferase expression in these pSDH-Tet-STAR10 clones(r=0.86). This suggests that STAR10 (SEQ ID NO:10) confers copynumber-dependence on the transgene expression units, making transgeneexpression independent of other transgene copies in tandem arrays andindependent of gene-silencing influences at the site of integration.

Example 10 STAR Elements Function as Enhancer Blockers but not Enhancers

Gene promoters are subject to both positive and negative influences ontheir ability to initiate transcription. An important class of elementsthat exert positive influences are enhancers. Enhancers arecharacteristically able to affect promoters even when they are locatedfar away (many kilobase pairs) from the promoter. Negative influencesthat act by heterochromatin formation (e.g., Polycomb group proteins)have been described above, and these are the target of STAR activity.The biochemical basis for enhancer function and for heterochromatinformation is fundamentally similar, since they both involve binding ofproteins to DNA. Therefore, it is important to determine whether STARelements are able to block positive influences as well as negativeinfluences, in other words, to shield transgenes from genomic enhancersin the vicinity of the site of integration. The ability to shieldtransgenes from enhancer activity ensures stable and predictableperformance of transgenes in biotechnological applications. This exampleexamines the performance of STAR elements in an enhancer-blocking assay.

Another feature of STAR activity that is important to their function isthe increased yield they confer on transgenes (Example 2). STARs areisolated on the basis of their ability to maintain high levels of zeocinexpression when heterochromatin-forming proteins are bound adjacent tothe candidate STAR elements. High expression is predicted to occurbecause STARs are anticipated to block the spread of heterochromatininto the zeocin expression unit. However, a second scenario is that theDNA fragments in zeocin-resistant clones contain enhancers. Enhancershave been demonstrated to have the ability to overcome the repressiveeffects of Polycomb-group proteins such as those used in the method ofthe STAR screen (Zink and Paro, 1995). Enhancers isolated by thisphenomenon would be considered false positives, since enhancers do nothave the properties claimed here for STARs. In order to demonstrate thatSTAR elements are not enhancers, they have been tested in an enhancerassay.

The enhancer-blocking assay and the enhancer assay are methodologicallyand conceptually similar. The assays are shown schematically in FIG. 13.The ability of STAR elements to block enhancers is performed using theE47/E-box enhancer system. The E47 protein is able to activatetranscription by promoters when it is bound to an E-box DNA sequencelocated in the vicinity of those promoters (Quong et al., 2002). E47 isnormally involved in regulation of B and T lymphocyte differentiation(Quong et al., 2002), but it is able to function in diverse cell typeswhen expressed ectopically (Petersson et al., 2002). The E-box is apalindromic DNA sequence, CANNTG (Knofler et al., 2002). In theenhancer-blocking assay, an E-box is placed upstream of a luciferasereporter gene (including a minimal promoter) in an expression vector. Acloning site for STAR elements is placed between the E-box and thepromoter. The E47 protein is encoded on a second plasmid. The assay isperformed by transfecting both the E47 plasmid and the luciferaseexpression vector into cells; the E47 protein is expressed and binds tothe E-box, and the E47/E-box complex is able to act as an enhancer. Whenthe luciferase expression vector does not contain a STAR element, theE47/E-box complex enhances luciferase expression (FIG. 13A, situation1). When STAR elements are inserted between the E-box and the promoter,their ability to block the enhancer is demonstrated by reducedexpression of luciferase activity (FIG. 13A, situation 2); if STARscannot block enhancers, luciferase expression is activated (FIG. 13A,situation 3).

The ability of STAR elements to act as enhancers utilizes the sameluciferase expression vector. In the absence of E47, the E-box itselfdoes not affect transcription. Instead, enhancer behavior by STARelements will result in activation of luciferase transcription. Theassay is performed by transfecting the luciferase expression vectorwithout the E47 plasmid. When the expression vector does not containSTAR elements, luciferase expression is low (FIG. 13B, situation 1). IfSTAR elements do not have enhancer properties, luciferase expression islow when a STAR element is present in the vector (FIG. 13B, situation2). If STAR elements do have enhancer properties, luciferase expressionwill be activated in the STAR-containing vectors (FIG. 13B, situation3).

Materials and Methods

The luciferase expression vector was constructed by inserting the E-boxand a human alkaline phosphatase minimal promoter from plasmidmu-E5+E2×6-cat(x) (Ruezinsky et al., 1991) upstream of the luciferasegene in plasmid pGL3-basic (Promega E1751), to createpGL3-E-box-luciferase (gift of W. Romanow). The E47 expression plasmidcontains the E47 open reading frame under control of a beta-actinpromoter in the pHBAPr-1-neo plasmid; E47 in constitutively expressedfrom this plasmid (gift of W. Romanow).

STAR elements 1, 2, 3, 6, 10, 11, 18, and 27 (SEQ ID NOS:1, 2, 3, 6, 10,11, 18, and 27, respectively) have been cloned into the luciferaseexpression vector. Clones containing the Drosophila scs element and thechicken beta-globin HS4-6× core (“HS4”) element have been included aspositive controls (they are known to block enhancers, and to have nointrinsic enhancer properties (Chung et al., 1993, Kellum and Schedl,1992)), and the empty luciferase expression vector has been included asa negative control. All assays were performed using the U-2 OS cellline. In the enhancer-blocking assay, the E47 plasmid was co-transfectedwith the luciferase expression vectors (empty vector, or containing STARor positive-control elements). In the enhancer assay, the E47 plasmidwas co-transfected with STARless luciferase expression vector as apositive control for enhancer activity; all other samples received amock plasmid during co-transfection. The transiently transfected cellswere assayed for luciferase activity 48 hours after plasmid transfection(supra). The luciferase activity expressed from a plasmid containing noE-box or STAR/control elements was subtracted, and the luciferaseactivities were normalized to protein content as described (supra).

Results

FIG. 14 shows the results of the enhancer-blocking assay. In the absenceof STAR elements (or the known enhancer-blocking elements scs and HS4),the E47/E-box enhancer complex activates expression of luciferase(“vector”); this enhanced level of expression has been normalized to100. Enhancer activity is blocked by all STAR elements tested. Enhanceractivity is also blocked by the HS4 and scs elements, as expected (Bellet al., 2001, Gerasimova and Corces, 2001). These results demonstratethat in addition to their ability to block the spreading oftranscriptional silencing (negative influences), STAR elements are ableto block the action of enhancers (positive influences).

FIG. 15 shows the results of the enhancer assay. The level of luciferaseexpression due to enhancement by the E47/E-box complex is set at 100(“E47”). By comparison, none of the STAR elements bring aboutsignificant activation of luciferase expression. As expected, the scsand HS4 elements also do not bring about activation of the reportergene. Therefore, it is concluded that at least the tested STAR elementsdo not possess enhancer properties.

Example 11 Star Elements are Conserved Between Mouse and Human

BLAT analysis of the STAR DNA sequence against the human genome database(http://genome.ucsc.edu/cgi-bin/hgGateway) reveals that some of thesesequences have high sequence conservation with other regions of thehuman genome. These duplicated regions are candidate STAR elements; ifthey do show STAR activity, they would be considered paralogs of thecloned STARs (two genes or genetic elements are said to be paralogous ifthey are derived from a duplication event (Li, 1997)).

BLAST analysis of the human STARs against the mouse genome(http://www.ensembl.org/Mus_musculus/blastview) also reveals regions ofhigh sequence conservation between mouse and human. This sequenceconservation has been shown for fragments of 15 out of the 65 human STARelements. The conservation ranges from 64% to 89%, over lengths of 141base pairs to 909 base pairs (Table 5). These degrees of sequenceconservation are remarkable and suggest that these DNA sequences mayconfer STAR activity within the mouse genome as well. Some of thesequences from the mouse and human genomes in Table 5 could be strictlydefined as orthologs (two genes or genetic elements are said to beorthologous if they are derived from a speciation event (Li, 1997)). Forexample, STAR6 (SEQ ID NO:6) is between the SLC8A1 and HAAO genes inboth the human and mouse genomes. In other cases, a cloned human STARhas a paralog within the human genome, and its ortholog has beenidentified in the mouse genome. For example, STAR3a is a fragment of the15q11.2 region of human chromosome 15. This region is 96.9% identical(paralogous) with a DNA fragment at 5q33.3 on human chromosome 5, whichis near the IL12B interleukin gene. These human DNAs share approximately80% identity with a fragment of the 11B2 region on mouse chromosome 11.The 11B2 fragment is also near the (mouse) IL12B interleukin gene.Therefore, STAR3a and the mouse 11B2 fragment can be strictly defined asparalogs.

In order to test the hypothesis that STAR activity is shared betweenregions of high sequence conservation in the mouse and human genome, oneof the human STARs with a conserved sequence in mouse, STAR18 (SEQ IDNO:18), has been analyzed in greater detail. The sequence conservationin the mouse genome detected with the original STAR18 clone extendsleftward on human chromosome 2 for about 500 base pairs (FIG. 16; leftand right relate to the standard description of the arms of chromosome2). In this example, we examine whether the region of sequenceconservation defines a “naturally occurring” STAR element in human thatis more extensive in length than the original clone. We also examinewhether the STAR function of this STAR element is conserved betweenmouse and human.

Materials and Methods

The region of mouse/human sequence conservation around STAR18 (SEQ IDNO:18) was recovered from human BAC clone RP11-387A1 by PCRamplification, in three fragments: the entire region (primers E93 (SEQID NO:171) and E94 (SEQ ID NO:172)), the leftward half (primers E93 (SEQID NO:171) and E92 (SEQ ID NO:170)), and the rightward half (primers E57(SEQ ID NO:169) and E94 (SEQ ID NO:172)). The corresponding fragmentsfrom the homologous mouse region were recovered from BAC cloneRP23-400H17 in the same fashion (primers E95 (SEQ ID NO:173) and E98(SEQ ID NO:176), E95 (SEQ ID NO:173) and E96 (SEQ ID NO:174), and E97(SEQ ID NO:175) and E98 (SEQ ID NO:176), respectively). All fragmentswere cloned into the pSelect vector and transfected into a U-2OS/Tet-Off/LexA-HP1 cell line (supra). Following transfection,hygromycin selection was carried out to select for transfected cells.The LexA-HP1 protein was induced by lowering the doxycyclineconcentration, and the ability of the transfected cells to withstand theantibiotic zeocin (a measure of STAR activity) was assessed bymonitoring cell growth.

Results

The original STAR18 clone was isolated from Sau3AI digested human DNAligated into the pSelect vector on the basis of its ability to preventsilencing of a zeocin resistance gene. Alignment of the human STAR18clone (497 base pairs) with the mouse genome revealed high sequencesimilarity (72%) between the orthologous human and mouse STAR18 (SEQ IDNO:18) regions. It also uncovered high similarity (73%) in the regionextending for 488 base pairs immediately to the left of the Sau3AI sitethat defines the left end of the cloned region (FIG. 16). Outside theseregions the sequence similarity between human and mouse DNA drops below60%.

As indicated in FIG. 16, both the human and the mouse STAR18 (SEQ IDNO:18) elements confer survival on zeocin to host cells expressing thelexA-HP1 repressor protein. The original 497 base pair STAR18 clone andits mouse ortholog both confer the ability to grow (FIG. 16, a and d).The adjacent 488 base pair regions of high similarity from both genomesalso confer the ability to grow, and in fact their growth phenotype ismore vigorous than that of the original STAR18 clone (FIG. 16, b and e).When the entire region of sequence similarity was tested, these DNAsfrom both mouse and human confer growth, and the growth phenotype ismore vigorous than the two sub-fragments (FIG. 16, c and f). Theseresults demonstrate that the STAR activity of human STAR18 (SEQ IDNO:18) is conserved in its ortholog from mouse. The high sequenceconservation between these orthologous regions is particularlynoteworthy because they are not protein-coding sequences, leading to theconclusion that they have some regulatory function that has preventedtheir evolutionary divergence through mutation.

This analysis demonstrates that cloned STAR elements identified by theoriginal screening program may in some cases represent partial STARelements, and that analysis of the genomic DNA in which they areembedded can identify sequences with stronger STAR activity.

Example 12 STAR Elements Contain Characteristic DNA Sequence Motifs

STAR elements are isolated on the basis of their anti-repressionphenotype with respect to transgene expression. This anti-repressionphenotype reflects underlying biochemical processes that regulatechromatin formation which are associated with the STAR elements. Theseprocesses are typically sequence-specific and result from proteinbinding or DNA structure. This suggests that STAR elements will shareDNA sequence similarity. Identification of sequence similarity amongSTAR elements will provide sequence motifs that are characteristic ofthe elements that have already been identified by functional screens andtests. The sequence motifs will also be useful to recognize and claimnew STAR elements whose functions conform to the claims of this patent.The functions include improved yield and stability of transgenesexpressed in eukaryotic host cells.

Other benefits of identifying sequence motifs that characterize STARelements include: (1) provision of search motifs for prediction andidentification of new STAR elements in genome databases, (2) provisionof a rationale for modification of the elements, and (3) provision ofinformation for functional analysis of STAR activity. Usingbio-informatics, sequence similarities among STAR elements have beenidentified; the results are presented in this example.

Bio-Informatic and Statistical Background

Regulatory DNA elements typically function via interaction withsequence-specific DNA-binding proteins. Bio-informatic analysis of DNAelements, such as STAR elements whose regulatory properties have beenidentified, but whose interacting proteins are unknown, requires astatistical approach for identification of sequence motifs. This can beachieved by a method that detects short DNA sequence patterns that areover-represented in a set of regulatory DNA elements (e.g., the STARelements) compared to a reference sequence (e.g., the complete humangenome). The method determines the number of observed and expectedoccurrences of the patterns in each regulatory element. The number ofexpected occurrences is calculated from the number of observedoccurrences of each pattern in the reference sequence.

The DNA sequence patterns can be oligonucleotides of a given length,e.g., six base pairs. In the simplest analysis, for a six-base-pairoligonucleotide (hexamer) composed of the four nucleotides (A, C, G, andT) there are 4⁶=4096 distinct oligonucleotides (all combinations fromAAAAAA (SEQ ID NO:121) to TTTTTT (SEQ ID NO:122)). If the regulatory andreference sequences were completely random and had equal proportions ofthe A, C, G, and T nucleotides, then the expected frequency of eachhexamer would be 1/4096 (˜0.00024). However, the actual frequency ofeach hexamer in the reference sequence is typically different than thisdue to biases in the content of G:C base pairs, etc. Therefore, thefrequency of each oligonucleotide in the reference sequence isdetermined empirically by counting, to create a “frequency table” forthe patterns.

The pattern frequency table of the reference sequence is then used tocalculate the expected frequency of occurrence of each pattern in theregulatory element set. The expected frequencies are compared with theobserved frequencies of occurrence of the patterns. Patterns that are“over-represented” in the set are identified; for example, if thehexamer ACGTGA (SEQ ID NO:123) is expected to occur five times in 20kilobase pairs of sequence, but is observed to occur 15 times, then itis three-fold over-represented. Ten of the 15 occurrences of thathexameric sequence pattern would not be expected in the regulatoryelements if the elements had the same hexamer composition as the entiregenome. Once the over-represented patterns are identified, a statisticaltest is applied to determine whether their over-representation issignificant, or may be due to chance. For this test, a significanceindex, “sig,” is calculated for each pattern. The significance index isderived from the probability of occurrence of each pattern, which isestimated by a binomial distribution. The probability takes into accountthe number of possible patterns (4096 for hexamers). The highest sigvalues correspond to the most overrepresented oligonucleotides (vanHelden et al., 1998). In practical terms, oligonucleotides with sig ≧0are considered as over-represented. A pattern with sig ≧0 is likely tobe over-represented due to chance once (=10⁰) in the set of regulatoryelement sequences. However, at sig ≧1 a pattern is expected to beover-represented once in ten (=10¹) sequence sets, sig ≧2 once in 100(=10²) sequence sets, etc.

The patterns that are significantly over-represented in the regulatoryelement set are used to develop a model for classification andprediction of regulatory element sequences. This employs DiscriminantAnalysis, a so-called “supervised” method of statistical classificationknown to one of ordinary skill in the art (Huberty, 1994). InDiscriminant Analysis, sets of known or classified items (e.g., STARelements) are used to “train” a model to recognize those items on thebasis of specific variables (e.g., sequence patterns such as hexamers).The trained model is then used to predict whether other items should beclassified as belonging to the set of known items (e.g., is a DNAsequence a STAR element). In this example, the known items in thetraining set are STAR elements (positive training set). They arecontrasted with sequences that are randomly selected from the genome(negative training set) which have the same length as the STAR elements.Discriminant Analysis establishes criteria for discriminating positivesfrom negatives based on a set of variables that distinguish thepositives; in this example, the variables are the significantlyover-represented patterns (e.g., hexamers).

When the number of over-represented patterns is high compared to thesize of the training set, the model could become biased due toover-training. Over-training is circumvented by applying a forwardstepwise selection of variables (Huberty, 1994). The goal of StepwiseDiscriminant Analysis is to select the minimum number of variables thatprovides maximum discrimination between the positives and negatives. Themodel is trained by evaluating variables one-by-one for their ability toproperly classify the items in the positive and negative training sets.This is done until addition of new variables to the model does notsignificantly increase the model's predictive power (i.e., until theclassification error rate is minimized). This optimized model is thenused for testing, in order to predict whether “new” items are positivesor negatives (Huberty, 1994).

It is inherent in classification statistics that for complex items suchas DNA sequences, some elements of the positive training set will beclassified as negatives (false negatives), and some members of thenegative training set will be classified as positives (false positives).When a trained model is applied to testing new items, the same types ofmisclassifications are expected to occur.

In the bio-informatic method described here, the first step, PatternFrequency Analysis, reduces a large set of sequence patterns (e.g., all4096 hexamers) to a smaller set of significantly over-representedpatterns (e.g., 100 hexamers); in the second step, Stepwise DiscriminantAnalysis reduces the set of over-represented patterns to the subset ofthose patterns that have maximal discriminative power (e.g., five to tenhexamers). Therefore, this approach provides simple and robust criteriafor identifying regulatory DNA elements such as STAR elements.

DNA-binding proteins can be distinguished on the basis of the type ofbinding site they occupy. Some recognize contiguous sequences; for thistype of protein, patterns that are oligonucleotides of length six basepairs (hexamers) are fruitful for bio-informatic analysis (van Helden etal., 1998). Other proteins bind to sequence dyads: contact is madebetween pairs of highly conserved trinucleotides separated by anon-conserved region of fixed width (van Helden et al., 2000). In orderto identify sequences in STAR elements that may be bound by dyad-bindingproteins, frequency analysis was also conducted for this type ofpattern, where the spacing between the two trinucleotides was variedfrom 0 to 20 (i.e., XXXN{0-20}XXX where X's are specific nucleotidescomposing the trinucleotides, and N's are random nucleotides from 0 to20 base pairs in length). The results of dyad frequency analysis arealso used for Linear Discriminant Analysis as described above.

Materials and Methods

Using the genetic screen described in the original patent application,sixty-six (66) STAR elements were initially isolated from human genomicDNA and characterized in detail (Table 3). The screen was performed ongene libraries constructed by Sau3AI digestion of human genomic DNA,either purified from placenta (Clontech 6550-1) or carried inbacterial/P1 (BAC/PAC) artificial chromosomes. The BAC/PAC clonescontain genomic DNA from regions of chromosome 1 (clones RP1154H19 andRP3328E19), from the HOX cluster of homeotic genes (clones RP1167F23,RP1170019, and RP11387A1), or from human chromosome 22 (ResearchGenetics 96010-22). The DNAs were size-fractionated, and the 0.5-2 kbsize fraction was ligated into BamHI-digested pSelect vector, bystandard techniques (Sambrook et al., 1989). pSelect plasmids containinghuman genomic DNA that conferred resistance to zeocin at low doxycyclineconcentrations were isolated and propagated in Escherichia coli. Thescreens that yielded the STAR elements of Table 3 have assayedapproximately 1-2% of the human genome.

The human genomic DNA inserts in these 66 plasmids were sequenced by thedideoxy method (Sanger et al., 1977) using a Beckman CEQ™2000 automatedDNA sequencer, using the manufacturer's instructions. Briefly, DNA waspurified from E. coli using QIAprep® Spin Miniprep and Plasmid Midi Kits(QIAGEN® 27106 and 12145, respectively). Cycle sequencing was carriedout using custom oligonucleotides corresponding to the pSelect vector(primers D89 (SEQ ID NO:149) and D95 (SEQ ID NO:154), Table 2), in thepresence of dye terminators (CEQ™ Dye Terminator Cycle Sequencing Kit,Beckman 608000). Assembled STAR DNA sequences were located in the humangenome (database builds August and December 2001) using BLAT (BasicLocal Alignment Tool (Kent, 2002);http://genome.ucsc.edu/cgi-bin/hgGateway; Table 3). In aggregate, thecombined STAR sequences comprise 85.6 kilobase pairs, with an averagelength of 1.3 kilobase pairs.

Sequence motifs that distinguish STAR elements within human genomic DNAwere identified by bio-informatic analysis using a two-step procedure,as follows (see FIG. 17 for a schematic diagram). The analysis has twoinput datasets: (1) the DNA sequences of the STAR elements (STAR1-STAR65(SEQ ID NOS:1-65) were used; Table 3); and (2) the DNA sequence of thehuman genome (except for chromosome 1, which was not feasible to includedue to its large size; for dyad analysis a random subset of humangenomic DNA sequence (˜27 Mb) was used).

Pattern Frequency Analysis

The first step in the analysis uses RSA-Tools software (RegulatorySequence Analysis Tools;http://www.ucmb.ulb.ac.be/bioinformatics/rsa-tools/; references (vanHelden et al., 1998, van Helden et al., 2000, van Helden et al., 2000))to determine the following information: (1) the frequencies of all dyadsand hexameric oligonucleotides in the human genome; (2) the frequenciesof the oligonucleotides and dyads in the 65 STAR elements; and (3) thesignificance indices of those oligonucleotides and dyads that areover-represented in the STAR elements compared to the genome. A controlanalysis was done with 65 sequences that were selected at random fromthe human genome (i.e., from 2689×10³ kilobase pairs) that match thelength of the STAR elements of Table 3.

Discriminant Analysis

The over-represented oligonucleotides and dyads were used to trainmodels for prediction of STAR elements by Linear Discriminant Analysis(Huberty, 1994). A pre-selection of variables was performed by selectingthe 50 patterns with the highest individual discriminatory power fromthe over-represented oligos or dyads of the frequency analyses. Thesepre-selected variables were then used for model training in a StepwiseLinear Discriminant Analysis to select the most discriminant combinationof variables (Huberty, 1994). Variable selection was based on minimizingthe classification error rate (percentage of false negativeclassifications). In addition, the expected error rate was estimated byapplying the same discriminant approach to the control set of randomsequences (minimizing the percentage of false positive classifications).

The predictive models from the training phase of Discriminant Analysiswere tested in two ways. First, the STAR elements and random sequencesthat were used to generate the model (the training sets) wereclassified. Second, sequences in a collection of 19 candidate STARelements (recently cloned by zeocin selection as described above) wereclassified. These candidate STAR elements are listed in Table 8 (SEQ IDNOS:66-84).

Results

Pattern frequency analysis was performed with RSA-Tools on 65 STARelements, using the human genome as the reference sequence. One hundredsixty-six (166) hexameric oligonucleotides were found to beover-represented in the set of STAR elements (sig ≧0) compared to theentire genome (Table 6). The most significantly over-representedoligonucleotide, CCCCAC (SEQ ID NO:177), occurs 107 times among the 65STAR elements, but is expected to occur only 49 times. It has asignificance coefficient of 8.76; in other words, the probability thatits over-representation is due to random chance is 1/10^(8.76), i.e.,less than one in 500 million.

Ninety-five of the oligonucleotides have a significance coefficientgreater than one, and are, therefore, highly over-represented in theSTAR elements. Among the over-represented oligonucleotides, theirobserved and expected occurrences, respectively, range from 6 and 1 (foroligo 163, CGCGAA (SEQ ID NO:339), sig=0.02) to 133 and 95 (for oligo120, CCCAGG (SEQ ID NO:296), sig=0.49). The differences in expectedoccurrences reflect factors such as the G:C content of the human genome.Therefore, the differences among the oligonucleotides in their number ofoccurrences is less important than their over-representation; forexample, oligo 2 (CAGCGG (SEQ ID NO:178)) is 36/9=four-foldover-represented, which has a probability of being due to random chanceof one in fifty million (sig=7.75).

Table 6 also presents the number of STAR elements in which eachover-represented oligonucleotide is found. For example, the mostsignificant oligonucleotide, oligo 1 (CCCCAC (SEQ ID NO:177)), occurs107 times, but is found in only 51 STARs, i.e., on average it occurs astwo copies per STAR. The least abundant oligonucleotide, number 166(AATCGG (SEQ ID NO:342)), occurs on average as a single copy per STAR(thirteen occurrences on eleven STARs); single-copy oligonucleotidesoccur frequently, especially for the lower-abundance oligos. At theother extreme, oligo 4 (CAGCCC (SEQ ID NO:527)) occurs on average threetimes in those STARs in which it is found (37 STARs). The mostwidespread oligonucleotide is number 120 (CCCAGG (SEQ ID NO:296)), whichoccurs on 58 STARs (on average twice per STAR), and the least widespreadoligonucleotide is number 114 (CGTCGC (SEQ ID NO:290)), which occurs ononly six STARs (and on average only once per STAR).

Results of dyad frequency analysis are given in Table 7. Seven hundredthirty (730) dyads were found to be over-represented in the set of STARelements (sig ≧0) compared to the reference sequence. The mostsignificantly over-represented dyad, CCCN{2}CGG (SEQ ID NO:343), occurs36 times among the 65 STAR elements, but is expected to occur only seventimes. It has a significance coefficient of 9.31; in other words, theprobability that its over-representation is due to chance is1/10^(9.31), i.e., less than one in two billion.

Three hundred ninety-seven (397) of the dyads have a significancecoefficient greater than 1, and are, therefore, highly over-representedin the STAR elements. Among the over-represented dyads, their observedand expected occurrences, respectively, range from 9 and 1 (for fivedyads (numbers 380, 435, 493, 640, and 665)) to 118 and 63 (for number30 (AGGN{2}GGG (SEQ ID NO:372)), sig=4.44).

The oligonucleotides and dyads found to be over-represented in STARelements by pattern frequency analysis were tested for theirdiscriminative power by Linear Discriminant Analysis. Discriminantmodels were trained by step-wise selection of the best combination amongthe 50 most discriminant oligonucleotide (Table 6) or dyad (Table 7)patterns. The models achieved optimal error rates after incorporation offour (dyad) or five variables. The discriminative variables from oligoanalysis are numbers 11, 30, 94, 122, and 160 (Table 6); those from dyadanalysis are numbers 73, 194, 419, and 497 (Table 7).

The discriminant models were then used to classify the 65 STAR elementsin the training set and their associated random sequences. The modelusing oligonucleotide variables classifies 46 of the 65 STAR elements asSTAR elements (true positives); the dyad model classifies 49 of the STARelements as true positives. In combination, the models classify 59 ofthe 65 STAR elements as STAR elements (91%; FIG. 18). The false positiverates (random sequences classified as STARs) were seven for the dyadmodel, eight for the oligonucleotide model, and 13 for the combinedpredictions of the two models (20%). The STAR elements of Table 3 thatwere not classified as STARs by LDA are STAR7, STAR22, STAR35, STAR44,STAR46, and STAR65 (SEQ ID NOS:7, 22, 35, 44, 46 and 65, respectively).These elements display stabilizing anti-repressor activity in functionalassays, so the fact that they are not classified as STARs by LDAsuggests that they represent another class (or classes) of STARelements.

The models were then used to classify the 19 candidate STAR elements inthe testing set listed in Table 8. The dyad model classifies 12 of thesecandidate STARs as STAR elements, and the oligonucleotide modelclassifies 14 as STARs. The combined number of the candidates that areclassified as STAR elements is 15 (79%). This is a lower rate ofclassification than obtained with the training set of 65 STARs; this isexpected for two reasons. First, the discriminant models were trainedwith the 65 STARs of Table 3, and discriminative variables based on thistraining set may be less well represented in the testing set. Second,the candidate STAR sequences in the testing set have not yet been fullycharacterized in terms of in vivo function, and may include elementswith only weak anti-repression properties.

This analysis demonstrates the power of a statistical approach tobio-informatic classification of STAR elements. The STAR sequencescontain a number of dyad and hexameric oligonucleotide patterns that aresignificantly over-represented in comparison with the human genome as awhole. These patterns may represent binding sites for proteins thatconfer STAR activity; in any case they form a set of sequence motifsthat can be used to recognize STAR element sequences.

Using these patterns to recognize STAR elements by DiscriminantAnalysis, a high proportion of the elements obtained by the geneticscreen of the invention are in fact classified as STARs. This reflectsunderlying sequence and functional similarities among these elements. Animportant aspect of the method described here (pattern frequencyanalysis followed by Discriminant Analysis) is that it can bereiterated; for example, by including the 19 candidate STAR elements ofTable 8 with the 66 STAR elements of Table 3 into one training set, animproved discriminant model can be trained. This improved model can thenbe used to classify other candidate regulatory elements as STARs.Large-scale in vivo screening of genomic sequences using the method ofthe invention, combined with reiteration of the bio-informatic analysis,will provide a means of discriminating STAR elements that asymptoticallyapproaches 100% recognition and prediction of elements as the genome isscreened in its entirety. These stringent and comprehensive predictionsof STAR function will ensure that all human STAR elements arerecognized, and are available for use in improving transgene expression.

Example 13 Cloning and Characterization of STAR Elements fromArabidopsis thaliana

Transgene silencing occurs in transgenic plants at both thetranscriptional and post-transcriptional levels (Meyer, 2000, Vance andVaucheret, 2001). In either case, the desired result of transgeneexpression can be compromised by silencing; the low expression andinstability of the transgene results in poor expression of desirabletraits (e.g., pest resistance) or low yields of recombinant proteins. Italso results in poor predictability: the proportion of transgenic plantsthat express the transgene at biotechnologically useful levels is low,which necessitates laborious and expensive screening of transformedindividuals for those with beneficial expression characteristics. Thisexample describes the isolation of STAR elements from the genome of thedicot plant Arabidopsis thaliana for use in preventing transcriptionaltransgene silencing in transgenic plants. Arabidopsis was chosen forthis example because it is a well-studied model organism: it has acompact genome, it is amenable to genetic and recombinant DNAmanipulations, and its genome has been sequenced (Bevan et al., 2001,Initiative, 2000, Meinke et al., 1998).

Materials and Methods

Genomic DNA was isolated from Arabidopsis thaliana ecotype Columbia asdescribed (Stam et al., 1998) and partially digested with MboI. Thedigested DNA was size-fractionated to 0.5-2 kilobase pairs by agarosegel electrophoresis and purification from the gel (QIAquick® GelExtraction Kit, QIAGEN® 28706), followed by ligation into the pSelectvector (supra). Transfection into the U-2 OS/Tet-Off/LexA-HP1 cell lineand selection for zeocin resistance at low doxycycline concentration wasperformed as described (supra). Plasmids were isolated from zeocinresistant colonies and re-transfected into the U-2 OS/Tet-Off/LexA-HP1cell line.

Sequencing of Arabidopsis genomic DNA fragments that conferred zeocinresistance upon re-transfection was performed as described (supra). TheDNA sequences were compared to the sequence of the Arabidopsis genome byBLAST analysis ((Altschul et al., 1990); URLhttp://www.ncbi.nlm.nih.gov/blast/Blast).

STAR activity was tested further by measuring mRNA levels for thehygromycin- and zeocin-resistance genes in recombinant host cells byreverse transcription PCR (RT-PCR). Cells of the U-2 OS/Tet-Off/lexA-HP1cell line were transfected with pSelect plasmids containing ArabidopsisSTAR elements, the Drosophila scs element, or containing no insert(supra). These were cultivated on hygromycin for two weeks at highdoxycycline concentration, then the doxycycline concentration waslowered to 0.1 ng/ml to induce the lexA-HP1 repressor protein. After tendays, total RNA was isolated by the RNeasy® mini kit (QIAGEN® 74104) asdescribed by the manufacturer. First-strand cDNA synthesis was carriedout using the RevertAid™ First Strand cDNA Synthesis kit (MBI Fermentas1622) using oligo(dT)18 primer as described by the manufacturer. Analiquot of the cDNA was used as the template in a PCR reaction usingprimers D58 (SEQ ID NO:145) and D80 (SEQ ID NO:148) (for the zeocinmarker), and D70 (SEQ ID NO:146) and D71 (SEQ ID NO:147) (for thehygromycin marker), and Taq DNA polymerase (Promega M2661). The reactionconditions were 15-20 cycles of 94° C. for one minute, 54° C. for oneminute, and 72° C. for 90 seconds. These conditions result in a linearrelationship between input RNA and PCR product DNA. The PCR productswere resolved by agarose gel electrophoresis, and the zeocin andhygromycin bands were detected by Southern blotting as described(Sambrook et al., 1989), using PCR products produced as above withpurified pSelect plasmid as template. The ratio of the zeocin andhygromycin signals corresponds to the normalized expression level of thezeocin gene.

Results

The library of Arabidopsis genomic DNA in the pSelect vector comprised69,000 primary clones in E. coli, 80% of which carried inserts. Theaverage insert size was approximately 1000 base pairs; the library,therefore, represents approximately 40% of the Arabidopsis genome.

A portion of this library (representing approximately 16% of theArabidopsis genome) was transfected into the U-2 OS/Tet-Off/LexA-HP1cell line. Hygromycin selection was imposed to isolate transfectants,which resulted in 27,000 surviving colonies. These were then subjectedto zeocin selection at low doxycycline concentration. PutativeSTAR-containing plasmids from 56 zeocin-resistant colonies were rescuedinto E. coli and re-transfected into U-2 OS/Tet-Off/LexA-HP1 cells.Forty-four of these plasmids (79% of the plasmids tested) conferredzeocin resistance on the host cells at low doxycycline concentrations,demonstrating that the plasmids carried STAR elements. This indicatesthat the pSelect screen in human U-2 OS cells is highly efficient atdetection of STAR elements from plant genomic DNA.

The DNA sequences of these 44 candidate STAR elements were determined.Thirty-five of them were identified as single loci in the database ofArabidopsis nuclear genomic sequence (Table 9; SEQ ID NO:85-SEQ IDNO:119). Four others were identified as coming from the chloroplastgenome, four were chimeras of DNA fragments from two loci, and one wasnot found in the Arabidopsis genome database.

The strength of the cloned Arabidopsis STAR elements was tested byassessing their ability to prevent transcriptional repression of thezeocin-resistance gene, using an RT-PCR assay. As a control for RNAinput among the samples, the transcript levels of thehygromycin-resistance gene for each STAR transfection were assessed too.This analysis has been performed for 12 of the Arabidopsis STARelements. The results (FIG. 19) demonstrate that the Arabidopsis STARelements are superior to the Drosophila scs element (positive control)and the empty vector (“SV40”; negative control) in their ability toprotect the zeocin-resistance gene from transcriptional repression. Inparticular, STAR-A28 (SEQ ID NO:112) and STAR-A30 (SEQ ID NO:114) enabletwo-fold higher levels of zeocin-resistance gene expression than the scselement (normalized to the internal control of hygromycin-resistancegene mRNA) when the lexA-HP1 repressor is expressed.

These results demonstrate that the method of the invention can besuccessfully applied to recovery of STAR elements from genomes of otherspecies than human. Its successful application to STAR elements from aplant genome is particularly significant because it demonstrates thewide taxonomic range over which the method of the invention isapplicable and because plants are an important target ofbiotechnological development.

Example 14 STAR Elements Function in CHO Cells

STAR elements function to block the effect of transcriptional repressioninfluences on transgene expression units. Two of the benefits of STARelements for heterologous protein production are an increasedpredictability to find high-expressing primary recombinant host cells aswell as increased protein production or yield in these cells.Importantly, the disclosed STAR elements are human DNA sequences,isolated in the human U-2 OS osteosarcoma cell line. It is, therefore,an important question whether the human STAR elements are functional ina) cell lines derived from species other than man, and/or in b) humancell lines other than the U-2 OS osteosarcoma cell line. In this examplethe functionality of STAR 7 (SEQ ID NO:7) in (CHO) Chinese hamster ovaryare illustrated.

Material and Methods

The STAR7 (SEQ ID NO:7) element is tested in the ppGIZ-STAR7 vector(FIG. 20). The construction of the pPlug&Play-GFP-ires-Zeo (ppGIZ)vector is described below. Plasmid pGFP (Clontech 6010-1) is modified byinsertion of a linker at the BsiWI site to yield pGFP-link. The linker(made by annealing oligonucleotides 5′ GTACGGATATCAGATCTTTAATTAAG 3′(SEQ ID NO:124) and 5′ GTACCTTAATTAAAGATCTGATATCC 3′ (SEQ ID NO:125))introduces sites for the PacI, BglII, and EcoRV restrictionendonucleases. This creates the multiple cloning site MCSII forinsertion of STAR elements. Then primers 5′ATCAGATCTGGCGCGCCATTTAAATCGTC TCGCGCGTTTCGGTGATGACGG 3′ (SEQ ID NO:126)and 5′ AGGCGGATCCGAATG TATTTAGAAAAATAAACAAATAGGGG 3′ (SEQ ID NO:127) areused to amplify a region of 0.37 kb from pGFP, which is inserted intothe BglII site of pIRES (Clontech 6028-1) to yield pIRES-stuf. Thisintroduces sites for the AscI and SwaI restriction endonucleases atMCSI, and acts as a “stuffer fragment” to avoid potential interferencebetween STAR elements and adjacent promoters. pIRES-stuf is digestedwith BglII and FspI to liberate a DNA fragment composed of the stufferfragment, the CMV promoter, the IRES element (flanked by multiplecloning sites MCS A and MCS B), and the SV40 polyadenylation signal.This fragment is ligated with the vector backbone of pGFP-link producedby digestion with BamHI and StuI, to yield pIRES-link.

The open reading frames of the zeocin-resistance gene is inserted intothe BamHI/NotI sites of MCS B in pIRES-link as follows: thezeocin-resistance ORF is amplified by PCR with primers 5′GATCGGATCCTTCGAAATGGCCAAGTTGACCAGTGC 3′ (SEQ ID NO:128) and 5′AGGCGCGGCCGCAATTCTCAGTCCTGCTCCTC 3′ (SEQ ID NO:129) from plasmidpEM7/zeo, digested with BamHI and NotI, and ligated withBamHI/NotI-digested pIRES-link to yield pIRES-link-zeo. The GFP reporterORF was introduced into pIRES-link-zeo by amplification of phr-GFP-1with primers 5′ GATCGAATTCTCGCGAATGGTGAGCAAGCAGATCCTGAAG 3′ (SEQ IDNO:130) and 5′ AGGCGAATTCACCGGTGTTTAAACTTACACCCACTCGTGCAGGCTGCCCAGG 3′(SEQ ID NO:131), and insertion of the EcoRI-digested GFP cassette intothe EcoRI site in MCS A of the pIRES-link-zeo plasmid. This created theppGIZ (for ppGFP-IRES-zeo). STAR7 (SEQ ID NO:7) is cloned into the SalIsite (5′) and into the PacI site (3′).

Transfection and Culture of CHO Cells

The Chinese Hamster Ovary cell line CHO-K1 (ATCC CCL-61) is cultured inHAMS-F12 medium+10% Fetal Calf Serum containing 2 mM glutamine, 100 U/mlpenicillin, and 100 micrograms/ml streptomycin at 37° C./5% CO₂. Cellsare transfected with the plasmids using Lipofectamine 2000 (Invitrogen)as described by the manufacturer. Briefly, cells are seeded to culturevessels and grown overnight to 70-90% confluence. Lipofectamine reagentis combined with plasmid DNA at a ratio of 7.5 microliters per 3microgram (e.g., for a 10 cm Petri dish, 20 micrograms DNA and 120microliters Lipofectamine) and added after a 30-minute incubation at 25°C. to the cells. After a six-hour incubation, the transfection mixtureis replaced with fresh medium, and the transfected cells are incubatedfurther. After overnight cultivation, cells are trypsinized and seededinto fresh petri dishes with fresh medium with zeocin added to aconcentration of 100 μg/ml and the cells are cultured further. Whenindividual colonies become visible (approximately ten days aftertransfection) medium is removed and replaced with fresh medium withoutzeocin. Individual clones are isolated and transferred to 24-well platesin medium with zeocin. Expression of the GFP reporter gene is assessedapproximately three weeks after transfection.

The tested constructs consist of a bicistronic gene with the GFP gene,an IRES and the Zeocin resistance gene under control of the CMVpromoter, but either with or without STAR7 (SEQ ID NO:7) element toflank the entire construct (FIG. 20). The constructs are transfected toCHO-K1 cells. Stable colonies are expanded before the GFP signal isdetermined on a XL-MCL Beckman Coulter flow cytometer. The mean of theGFP signal is taken as measure for the level of GFP expression and thisis plotted in FIG. 20.

Results

FIG. 20 shows that flanking a GFP reporter gene that is under thecontrol of the CMV promoter results in a higher number of CHO coloniesthat express significantly higher levels of GFP protein, as compared tothe control without STAR7 (SEQ ID NO:7) element. The STAR7 (SEQ ID NO:7)element, therefore, conveys a higher degree of predictability oftransgene expression in CHO cells. The highest GFP expression level inSTAR-shielded CHO colonies is also higher than in STAR-less controlcolonies. In addition, when the tested colonies were further grown foranother 30 days without Zeocin in the culture medium, the GFP expressionlevels in the STAR-shielded colonies remained equally high, whereas theGFP expression levels in the STAR-less colonies dropped to at leastbelow 50% of the original values. It is, therefore, concluded that STAR7(SEQ ID NO:7) is able to convey higher as well as more stable expressionlevels to a transgene in CHO cells, this being a cell line derived fromanother species than man.

Example 15 STAR Elements Function in NSO Cells

STAR elements function to block the effect of transcriptional repressioninfluences on transgene expression units. Two of the benefits of STARelements for heterologous protein production are an increasedpredictability to find high-expressing primary recombinant host cells,as well as increased protein production or yield in these cells.Importantly, the disclosed STAR elements are human DNA sequences,isolated in the human U-2 OS osteosarcoma cell line. It is, therefore,an important question whether the human STAR elements are functional ina) cell lines derived from species other than man, and/or in b) humancell lines other than the U-2 OS osteosarcoma cell line. In this examplethe functionality of STAR 7 (SEQ ID NO:7) in non-secreting mouse myeloma(NSO) cells are illustrated.

Materials and Methods

The tested constructs are the same as described in Example 14. NSO(Non-Secreting mouse myeloma) cells (ECACC 85110503) are suspensioncells that are cultured in RPMI 1640 medium+10% Fetal Calf Serumcontaining 2 mM glutamine, 100 U/ml penicillin, and 100 micrograms/mlstreptomycin at 37° C./5% CO₂. Cells are transfected with the plasmidsusing Lipofectamine 2000 (Invitrogen) as described by the manufacturer.Briefly, cells are seeded to culture vessels and grown overnight to4×10⁵/ml. Lipofectamine reagent is combined with plasmid DNA at a ratioof 3 microliters per microgram DNA (e.g., for a 10 cm Petri dish, 20micrograms DNA and 60 microliters Lipofectamine) and added after 30minutes incubation at 25° C. temperature to the cells. After overnightincubation, the transfection mixture is replaced with fresh medium andthe transfected cells are incubated further. After another overnightincubation, zeocin is added to a concentration of 100 μg/ml and thecells are cultured and further incubated for three days. Then the cellsare seeded in 96-well plates in such dilutions that one well willcontain ˜1 cell. After ten days growing colonies are transferred to24-well plates.

Results

FIG. 21 shows that flanking a GFP reporter gene that is under thecontrol of the CMV promoter results in a higher number of NSO coloniesthat express significantly higher levels of GFP protein, as compared tothe control without STAR7 (SEQ ID NO:7) element. The STAR7 (SEQ ID NO:7)element, therefore, conveys a higher degree of predictability oftransgene expression in NSO cells. The highest GFP expression level inSTAR-shielded NSO colonies is also higher than in STAR-less controlcolonies. It is, therefore, concluded that STAR7 (SEQ ID NO:7) is ableto convey higher expression levels to a transgene in NSO cells, thisbeing a cell line derived from another species than man.

Example 16 STAR Elements Function in Human 293 Cells

STAR elements function to block the effect of transcriptional repressioninfluences on transgene expression units. Two of the benefits of STARelements for heterologous protein production are an increasedpredictability to find high-expressing primary recombinant host cells aswell as increased protein production or yield in these cells.Importantly, the disclosed STAR elements are human DNA sequences,isolated in the human U-2 OS osteosarcoma cell line. It is, therefore,an important question whether the human STAR elements are functional ina) cell lines derived from species other than man, and/or in b) humancell lines other than the U-2 OS osteosarcoma cell line. In thisexample, the functionality of STAR7 (SEQ ID NO:7) in human 293 cells areillustrated.

Materials and Methods

The tested constructs are the same as described in Example 14. The 293cell line (ATCC CRL-1573) is derived from human embryonal kidney(immortalized by adenovirus 5 transfection) and is cultured inDulbecco's Modified Eagle Medium+10% Fetal Calf Serum containing 2 mMglutamine, 100 U/ml penicillin, and 100 micrograms/ml streptomycin at37° C./5% CO₂. Cells are transfected with the plasmids usingLipofectamine 2000 (Invitrogen) as described by the manufacturer.Selection and propagation of the 293 colonies are as described inExample 14 for U-2 OS cells.

Results

FIG. 22 shows that flanking a GFP reporter gene that is under thecontrol of the CMV promoter results in a higher number of 293 coloniesthat express significantly higher levels of GFP protein, as compared tothe control without STAR7 (SEQ ID NO:7) element. The STAR7 (SEQ ID NO:7)element, therefore, conveys a higher degree of predictability oftransgene expression in 293 cells. The highest GFP expression level inSTAR-shielded colonies is also higher than in STAR-less controlcolonies. It is, therefore, concluded that STAR7 (SEQ ID NO:7) is ableto convey higher expression levels to a transgene in 293 cells, thisbeing another human cell line, distinct from the human U-2 OS cell line.

TABLE 1 Biopharmaceutical Proteins, Their Tissue or Cell Type of OriginProtein Tissue/Somatic Cells Cell Lines (ATCC #)¹ Indications alpha-1Antitrypsin Liver, leukocytes Hep G2 (HB-8065) Cystic fibrosis,emphysema alpha-Galactosidase A; -Glucosidase Fibroblasts WI 38 (CCL-75)Fabry disease; Pompe's disease Antibodies (monoclonal, LymphocytesTransfectomas Various therapeutic single-chain, etc) strategiesAntithrombin III Liver Hep G2 (HB-8065) Thrombophilia Calcitonin Thyroid(parafollicular cells) TT (CRL-1803) Osteoporosis Ciliary neurotrophicfactor Neural tissue (e.g., astrocytes) HCN-1A (CRL-10442) Motor neurondisease Epidermal Growth Factor Kidney G-401 (CRL-1441) Wound healingErythropoietin Liver, kidney Hep G2 (HB-8065), Anemia G-401 (CRL-1441)Factors VII, VIII, IX Endothelial cells HUV-EC-C (CRL-1730) HemophiliaFamoxin (recombinant gAcrp30) Adipocytes NA² Obesity Fibroblast growthfactor (basic) Cerebral cortex, hypothalamus HCN-1A (CRL-10442) Woundhealing, angiogenesis Gastric lipase Pancreas BxPC-3 (CRL-1687)Pancreatic insufficiency, cystic fibrosis Glucocerebrosidase MacrophagesU-937 (CRL-1593.2) Gaucher disease Granulocyte macrophage-colonyT-lymphocytes J.CaM1.6 (CRL-2063) Chemotherapy neutropenia stimulatinfactor Human growth hormone Pituitary gland HP75 (CRL-2506) Growthretardation, Turner's (somatotropin) syndrome Human serum albumin Liver(hepatocytes) Hep G2 (HB-8065) Blood replacement (surgery, burns)Insulin Pancreas (Islet beta cells) BxPC-3 (CRL-1687) DiabetesInterferons alpha Leukocytes WBC264-9C (HB-8902) Cancer, hepatitis CInterferons beta Fibroblasts WI 38 (CCL-75) Multiple sclerosisInterleukin-2, -4, -10 T-lymphocytes J.CaM1.6 (CRL-2063) Cancer,rheumatoid arthritis, hepatitis Interleukin-18 Monocytes and macrophagesU-937 (CRL-1593.2) Cancer, bacterial infections Interleukin-1 ReceptorAntagonist Epithelium HBE4-E6/E7 (CRL-2078) Rheumatoid arthritis SolubleTumor Necrosis Factor Placenta, spleen, fibroblasts BeWo (CCL-98)Rheumatoid arthritis, receptor multiple sclerosis van Willebrand'sfactor Endothelial cells HUV-EC-C (CRL-1730) Hemophilia ¹These celllines are offered only as examples of cultured cells corresponding tothe tissues and somatic cells; ATCC #: American Type Culture Collectionaccession number ²NA: Not Available; adipocytes can be differentiatedfrom various other cell types

TABLE 2 Oligonucleotides used for polymerase chain reactions (PCRprimers) or DNA mutagenesis (SEQ ID NOS:134-176) SEQ ID NO: NumberSequence 134 C65 AACAAGCTTGATATCAGATCTGCTAGCTTGGT CGAGCTGATACTTCCC 135C66 AAACTCGAGCGGCCGCGAATTCGTCGACTTTA CCACTCCCTATCAGTGATAGAG 136 C67AAACCGCGGCATGGAAGACGCCAAAAACATAA AGAAAGG 137 C68TATGGATCCTAGAATTACACGGCGATCTTTCC 138 C81 AAACCATGGCCGAGTACAAGCCCACGGTGCGCC 139 C82 AAATCTAGATCAGGCACCGGGCTTGCGGGTCA TGC 140 C85CATTTCCCCGAAAAGTGCCACC 141 D30 TCACTGCTAGCGAGTGGTAAACTC 142 D41GAAGTCGACGAGGCAGGCAGAAGTATGC 143 D42 GAGCCGCGGTTTAGTTCCTCACCTTGTCG 144D51 TCTGGAAGCTTTGCTGAAGAAAC 145 D58 CCAAGTTGACCAGTGCC 146 D70TACAAGCCAACCACGGCCT 147 D71 CGGAAGTGCTTGACATTGGG 148 D80GTTCGTGGACACGACCTCCG 149 D89 GGGCAAGATGTCGTAGTCAGG 150 D90AGGCCCATGGTCACCTCCATCGCTACTGTG 151 D91 CTAATCACTCACTGTGTAAT 152 D93AATTACAGGCGCGCC 153 D94 AATTGGCGCGCCTGT 154 D95TGCTTTGCATACTTCTGCCTGCCTC 155 E12 TAGGGGGGATCCAAATGTTC 156 E13CCTAAAAGAAGATCTTTAGC 157 E14 AAGTGTTGGATCCACTTTGG 158 E15TTTGAAGATCTACCAAATGG 159 E16 GTTCGGGATCCACCTGGCCG 160 E17TAGGCAAGATCTTGGCCCTC 161 E18 CCTCTCTAGGGATCCGACCC 162 E19CTAGAGAGATCTTCCAGTAT 163 E20 AGAGTTCCGGATCCGCCTGG 164 E21CCAGGCAGACTCGGAACTCT 165 E22 TGGTGAAACCGGATCCCTAC 166 E23AGGTCAGGAGATCTAGACCA 167 E25 CCATTTTCGCTTCCTTAGCTCC 168 E42CGATGTAACCCACTCGTGCACC 169 E57 AGAGATCTAGGATAATTTCG 170 E92AGGCGCTAGCACGCGTTCTACTCTTTTCCTAC TCTG 171 E93GATCAAGCTTACGCGTCTAAAGGCATTTTATA TAG 172 E94AGGCGCTAGCACGCGTTCAGAGTTAGTGATCC AGG 173 E95GATCAAGCTTACGCGTCAGTAAAGGTTTCGTA TGG 174 E96AGGCGCTAGCACGCGTTCTACTCTTTCATTAC TCTG 175 E97 CGAGGAAGCTGGAGAAGGAGAAGCTG176 E98 CAAGGGCCGCAGCTTACACATGTTC

TABLE 3 STAR elements of the invention, including genomic location andlength (SEQ ID NOS: 1-66) STAR SEQ ID NO: Location¹ Length 1 1 2q31.1750 2 2 7p15.2 916 3 3 15q11.2 and 10q22.2 2132 4 4 1p31.1 and 14q24.11625 5 5 20q13.32 1571 6 6 2p21 1173 7 7 1q34 2101 8 8 9q32 1839 9 910p15.3 1936 10 10 Xp11.3 1167 11 11 2p25.1 1377 12 12 5q35.3 1051 13 139q34.3 1291 14 14 22q11.22 732 15 15 1p36.31 1881 16 16 1p21.2 1282 1717 2q31.1 793 18 18 2q31.3 497 19 19 6p22.1 1840 20 20 8p13.3 780 21 216q24.2 620 22 22 2q12.2 1380 23 23 6p22.1 1246 24 24 1q21.2 948 25 251q21.3 1067 26 26 1q21.1 540 27 27 1q23.1 1520 28 28 22q11.23 961 29 292q13.31 2253 30 30 22q12.3 1851 31 31 9q34.11 and 22q11.21 1165 32 3221q22.2 771 33 33 21q22.2 1368 34 34 9q34.14 755 35 35 7q22.3 1211 36 3621q22.2 1712 37 37 22q11.23 1331 38 38 22q11.1 and 22q11.1 ~1000 39 3922q12.3 2331 40 40 22q11.21 1071 41 41 22q11.21 1144 42 42 22q11.1 73543 43 14q24.3 1231 44 44 22q11.1 1591 45 45 22q11.21 1991 46 46 22q11.231871 47 47 22q11.21 1082 48 48 22q11.22 1242 49 49 Chr 12 random clone,and 1015 3q26.32 50 50 6p21.31 2361 51 51 5q21.3 2289 52 52 7p15.2 120053 53 Xp11.3 1431 54 54 4q21.1 981 55 55 15q13.1 501 56 56 includes3p25.3 741 57 57 4q35.2 1371 58 58 21q11.2 1401 59 59 17 random clone872 60 60 4p16.1 and 6q27 2068 61 61 7p14.3 and 11q25 1482 62 62 14q24.31011 63 63 22q13.3 1421 64 64 17q11.2 1414 65 65 7q21.11 = 28.4 1310 6666 20q13.33 and 6q14.1 ~2800 ¹Chromosomal location is determined byBLAST search of DNA sequence data from the STAR elements against thehuman genome database. The location is given according to standardnomenclature referring to the cytogenetic ideogram of each chromosome;e.g., 1p2.3 is the third cytogenetic sub-band of the second cytogeneticband of the short arm of chromosome 1(http://www.ncbi.nlm.nih.gov/Class/MLACourse/Genetics/chrombanding.html).F, forward sequencing reaction result; R, reverse sequencing reactionresult.

TABLE 4 STAR elements convey stability over time on transgeneexpression¹ Cell Divisions² Luciferase Expression³ STAR6 (SEQ ID NO: 6)42 18,000 plus puromycin 60 23,000 84 20,000 108 16,000 STAR6 (SEQ IDNO: 6) 84 12,000 without puromycin⁴ 108 15,000 144 12,000 ¹PlasmidpSDH-Tet-STAR6 was transfected into U-2 OS cells, and clones wereisolated and cultivated in doxycycline-free medium as described inExample 1. Cells were transferred to fresh culture vessels weekly at adilution of 1:20. ²The number of cell divisions is based on theestimation that in one week the culture reaches cell confluence, whichrepresents ~6 cell divisions. ³Luciferase was assayed as described inExample 1. ⁴After 60 cell divisions the cells were transferred to twoculture vessels; one was supplied with culture medium that containedpuromycin, as for the first 60 cell divisions, and the second wassupplied with culture medium lacking antibiotic.

TABLE 5 Human STAR elements and their putative mouse orthologs andparalogs NUMBER STAR Human¹ Mouse² Similarity³ SEQ ID NO: 1  1 2q31.1 2D600 bp 69% 1 2  2 7p15.2 6B3 909 bp 89% 2 3  3a 5q33.3 11B2 248 bp 83% 34  3b 10q22.2 14B 1. 363 bp 89% 3 2. 163 bp 86% 5  6 2p21 17E4 437 bp78% 6 6 12 5q35.3 11b1.3 796 bp 66% 12 7 13 9q34.3 2A3 753 bp 77% 13 818 2q31.3 2E1 497 bp 72% 18 9 36 21q22.2 16C4 166 bp 79% 36 10 4022q11.1 6F1 1. 270 bp 75% 40 2. 309 bp 70% 11 50 6p21.31 17B1 1. 451 bp72% 50 2. 188 bp 80% 3. 142 bp 64% 12 52 7p15.2 6B3 1. 846 bp 74% 52 2.195 bp 71% 13 53 Xp11.3 XA2 364 bp 64% 53 14 54 4q21.1 5E3 1. 174 bp 80%54 2. 240 bp 73% 3. 141 bp 67% 4. 144 bp 68% 15 61a 7p14.3 6B3 188 bp68% 61 ¹Cytogenetic location of STAR element in the human genome.²Cytogenetic location of STAR element ortholog in the mouse genome.³Length of region(s) displaying high sequence similarity, and percentagesimilarity. In some cases more than one block of high similarity occurs;in those cases, each block is described separately. Similarity <60% isnot considered significant.

The patterns are ranked according to significance coefficient. Thesewere determined using RSA-Tools with the sequence of the human genome asreference. Patterns that comprise the most discriminant variables inLinear Discriminant Analysis are indicated with an asterisk. (SEQ IDNOS:177-342)

TABLE 6 Oligonucleotide patterns (6 base pairs) over-represented in STARelements. Number of Oligonucleotide Observed Expected Significancematching SEQ ID Number sequence occurrences occurrences coefficientSTARs NO: 1 CCCCAC 107 49 8.76 51 177 2 CAGCGG 36 9 7.75 23 178 3 GGCCCC74 31 7.21 34 179 4 CAGCCC 103 50 7.18 37 180 5 GCCCCC 70 29 6.97 34 1816 CGGGGC 40 12 6.95 18 182 7 CCCCGC 43 13 6.79 22 183 8 CGGCAG 35 9 6.6418 184 9 AGCCCC 83 38 6.54 40 185 10 CCAGGG 107 54 6.52 43 186 11GGACCC * 58 23 6.04 35 187 12 GCGGAC 20 3 5.94 14 188 13 CCAGCG 34 105.9 24 189 14 GCAGCC 92 45 5.84 43 190 15 CCGGCA 28 7 5.61 16 191 16AGCGGC 27 7 5.45 17 192 17 CAGGGG 86 43 5.09 43 193 18 CCGCCC 43 15 5.0218 194 19 CCCCCG 35 11 4.91 20 195 20 GCCGCC 34 10 4.88 18 196 21 GCCGGC22 5 4.7 16 197 22 CGGACC 19 4 4.68 14 198 23 CGCCCC 35 11 4.64 19 19924 CGCCAG 28 8 4.31 19 200 25 CGCAGC 29 8 4.29 20 201 26 CAGCCG 32 10 424 202 27 CCCACG 33 11 3.97 26 203 28 GCTGCC 78 40 3.9 43 204 29 CCCTCC106 60 3.87 48 205 30 CCCTGC * 92 50 3.83 42 206 31 CACCCC 77 40 3.75 40207 32 GCGCCA 30 10 3.58 23 208 33 AGGGGC 70 35 3.55 34 209 34 GAGGGC 6632 3.5 40 210 35 GCGAAC 14 2 3.37 13 211 36 CCGGCG 17 4 3.33 12 212 37AGCCGG 34 12 3.29 25 213 38 GGAGCC 67 34 3.27 40 214 39 CCCCAG 103 603.23 51 215 40 CCGCTC 24 7 3.19 19 216 41 CCCCTC 81 44 3.19 43 217 42CACCGC 33 12 3.14 22 218 43 CTGCCC 96 55 3.01 42 219 44 GGGCCA 68 352.99 39 220 45 CGCTGC 28 9 2.88 22 221 46 CAGCGC 25 8 2.77 19 222 47CGGCCC 28 10 2.73 19 223 48 CCGCCG 19 5 2.56 9 224 49 CCCCGG 30 11 2.4117 225 50 AGCCGC 23 7 2.34 17 226 51 GCACCC 55 27 2.31 38 227 52 AGGACC54 27 2.22 33 228 53 AGGGCG 24 8 2.2 18 229 54 CAGGGC 81 47 2.18 42 23055 CCCGCC 45 21 2.15 20 231 56 GCCAGC 66 36 2.09 39 232 57 AGCGCC 21 62.09 18 233 58 AGGCCC 64 34 2.08 32 234 59 CCCACC 101 62 2.05 54 235 60CGCTCA 21 6 2.03 17 236 61 AACGCG 9 1 1.96 9 237 62 GCGGCA 21 7 1.92 14238 63 AGGTCC 49 24 1.87 36 239 64 CCGTCA 19 6 1.78 14 240 65 CAGAGG 10768 1.77 47 241 66 CCCGAG 33 14 1.77 22 242 67 CCGAGG 36 16 1.76 25 24368 CGCGGA 11 2 1.75 8 244 69 CCACCC 87 53 1.71 45 245 70 CCTCGC 23 81.71 20 246 71 CAAGCC 59 32 1.69 40 247 72 TCCGCA 18 5 1.68 17 248 73CGCCGC 18 5 1.67 9 249 74 GGGAAC 55 29 1.63 39 250 75 CCAGAG 93 58 1.5749 251 76 CGTTCC 19 6 1.53 16 252 77 CGAGGA 23 8 1.5 19 253 78 GGGACC 4824 1.48 31 254 79 CCGCGA 10 2 1.48 8 255 80 CCTGCG 24 9 1.45 17 256 81CTGCGC 23 8 1.32 14 257 82 GACCCC 47 24 1.31 33 258 83 GCTCCA 66 38 1.2539 259 84 CGCCAC 33 15 1.19 21 260 85 GCGGGA 23 9 1.17 18 261 86 CTGCGA18 6 1.15 15 262 87 CTGCTC 80 49 1.14 50 263 88 CAGACG 23 9 1.13 19 26489 CGAGAG 21 8 1.09 17 265 90 CGGTGC 18 6 1.06 16 266 91 CTCCCC 84 531.05 47 267 92 GCGGCC 22 8 1.04 14 268 93 CGGCGC 14 4 1.04 13 269 94AAGCCC * 60 34 1.03 42 270 95 CCGCAG 24 9 1.03 17 271 96 GCCCAC 59 340.95 35 272 97 CACCCA 92 60 0.93 49 273 98 GCGCCC 27 11 0.93 18 274 99ACCGGC 15 4 0.92 13 275 100 CTCGCA 16 5 0.89 14 276 101 ACGCTC 16 5 0.8812 277 102 CTGGAC 58 33 0.88 32 278 103 GCCCCA 67 40 0.87 38 279 104ACCGTC 15 4 0.86 11 280 105 CCCTCG 21 8 0.8 18 281 106 AGCCCG 22 8 0.7914 282 107 ACCCGA 16 5 0.78 13 283 108 AGCAGC 79 50 0.75 41 284 109ACCGCG 14 4 0.69 7 285 110 CGAGGC 29 13 0.69 24 286 111 AGCTGC 70 430.64 36 287 112 GGGGAC 49 27 0.64 34 288 113 CCGCAA 16 5 0.64 12 289 114CGTCGC 8 1 0.62 6 290 115 CGTGAC 17 6 0.57 15 291 116 CGCCCA 33 16 0.5622 292 117 CTCTGC 97 65 0.54 47 293 118 AGCGGG 21 8 0.52 17 294 119ACCGCT 15 5 0.5 11 295 120 CCCAGG 133 95 0.49 58 296 121 CCCTCA 71 450.49 39 297 122 CCCCCA * 77 49 0.49 42 298 123 GGCGAA 16 5 0.48 14 299124 CGGCTC 29 13 0.47 19 300 125 CTCGCC 20 8 0.46 17 301 126 CGGAGA 20 80.45 14 302 127 TCCCCA 95 64 0.43 52 303 128 GACACC 44 24 0.42 33 304129 CTCCGA 17 6 0.42 13 305 130 CTCGTC 17 6 0.42 14 306 131 CGACCA 13 40.39 11 307 132 ATGACG 17 6 0.37 12 308 133 CCATCG 17 6 0.37 13 309 134AGGGGA 78 51 0.36 44 310 135 GCTGCA 77 50 0.35 43 311 136 ACCCCA 76 490.33 40 312 137 CGGAGC 21 9 0.33 16 313 138 CCTCCG 28 13 0.32 19 314 139CGGGAC 16 6 0.3 10 315 140 CCTGGA 88 59 0.3 45 316 141 AGGCGA 18 7 0.2917 317 142 ACCCCT 54 32 0.28 36 318 143 GCTCCC 56 34 0.27 36 319 144CGTCAC 16 6 0.27 15 320 145 AGCGCA 16 6 0.26 11 321 146 GAAGCC 62 380.25 39 322 147 GAGGCC 79 52 0.22 42 323 148 ACCCTC 54 32 0.22 33 324149 CCCGGC 37 20 0.21 21 325 150 CGAGAA 20 8 0.2 17 326 151 CCACCG 29 140.18 20 327 152 ACTTCG 16 6 0.17 14 328 153 GATGAC 48 28 0.17 35 329 154ACGAGG 23 10 0.16 18 330 155 CCGGAG 20 8 0.15 18 331 156 ACCCAC 60 370.12 41 332 157 CTGGGC 105 74 0.11 50 333 158 CCACGG 23 10 0.09 19 334159 CGGTCC 13 4 0.09 12 335 160 AGCACC * 54 33 0.09 40 336 161 ACACCC 5332 0.08 38 337 162 AGGGCC 54 33 0.08 30 338 163 CGCGAA 6 1 0.02 6 339164 GAGCCC 58 36 0.02 36 340 165 CTGAGC 71 46 0.02 45 341 166 AATCGG 134 0.02 11 342

The patterns are ranked according to significance coefficient. Thesewere determined using RSA-Tools with the random sequence from the humangenome as reference. Patterns that comprise the most discriminantvariables in Linear Discriminant Analysis are indicated with anasterisk. (SEQ ID NOS:343-1072)

TABLE 7 Dyad patterns over-represented in STAR elements. ObservedExpected Significance SEQ ID Number Dyad sequence occurrencesoccurrences coefficient NO: 1 CCCN{2}CGG 36 7 9.31 343 2 CCGN{6}CCC 4010 7.3 344 3 CAGN{0}CGG 36 8 7.13 345 4 CGCN{15}CCC 34 8 6.88 346 5CGGN{9}GCC 33 7 6.82 347 6 CCCN{9}CGC 35 8 6.72 348 7 CCCN{1}GCG 34 86.64 349 8 CCCN{0}CAC 103 48 6.61 350 9 AGCN{16}CCG 29 6 5.96 351 10CCCN{4}CGC 34 8 5.8 352 11 CGCN{13}GGA 26 5 5.77 353 12 GCGN{16}CCC 30 75.74 354 13 CGCN{5}GCA 25 5 5.49 355 14 CCCN{14}CCC 101 49 5.43 356 15CTGN{4}CGC 34 9 5.41 357 16 CCAN{12}GCG 28 6 5.37 358 17 CGGN{11}CAG 3610 5.25 359 18 CCCN{5}GCC 75 33 4.87 360 19 GCCN{0}CCC 64 26 4.81 361 20CGCN{4}GAC 19 3 4.78 362 21 CGGN{0}CAG 33 9 4.76 363 22 CCCN{3}CGC 32 84.67 364 23 CGCN{1}GAC 20 3 4.58 365 24 GCGN{2}GCC 29 7 4.54 366 25CCCN{4}GCC 76 34 4.53 367 26 CCCN{1}CCC 103 52 4.53 368 27 CCGN{13}CAG33 9 4.5 369 28 GCCN{4}GGA 64 27 4.48 370 29 CCGN{3}GGA 26 6 4.46 371 30AGGN{2}GGG 118 63 4.44 372 31 CACN{5}GCG 22 4 4.42 373 32 CGCN{17}CCA 276 4.39 374 33 CCCN{9}GGC 69 30 4.38 375 34 CCTN{5}GCG 28 7 4.37 376 35GCGN{0}GAC 19 3 4.32 377 36 GCCN{0}GGC 40 7 4.28 378 37 GCGN{2}CCC 26 64.27 379 38 CCGN{11}CCC 32 9 4.17 380 39 CCCN{8}TCG 23 5 4.12 381 40CCGN{17}GCC 30 8 4.12 382 41 GGGN{5}GGA 101 52 4.11 383 42 GGCN{6}GGA 7132 4.1 384 43 CCAN{4}CCC 96 48 4.1 385 44 CCTN{14}CCG 32 9 4.09 386 45GACN{12}GGC 45 16 4.07 387 46 CGCN{13}CCC 30 8 4.04 388 47 CAGN{16}CCC92 46 4.02 389 48 AGCN{10}GGG 75 35 3.94 390 49 CGGN{13}GGC 30 8 3.93391 50 CGGN{1}GCC 30 8 3.92 392 51 AGCN{0}GGC 26 6 3.9 393 52CCCN{16}GGC 64 28 3.89 394 53 GCTN{19}CCC 67 29 3.87 395 54 CCCN{16}GGG88 31 3.81 396 55 CCCN{9}CGG 30 8 3.77 397 56 CCCN{10}CGG 30 8 3.76 39857 CCAN{0}GCG 32 9 3.75 399 58 GCCN{17}CGC 26 6 3.74 400 59 CCTN{6}CGC27 7 3.73 401 60 GGAN{1}CCC 63 27 3.71 402 61 CGCN{18}CAC 24 5 3.7 40362 CGCN{20}CCG 21 4 3.69 404 63 CCGN{0}GCA 26 6 3.69 405 64 CGCN{20}CCC28 7 3.69 406 65 AGCN{15}CCC 67 30 3.65 407 66 CCTN{7}GGC 69 31 3.63 40867 GCCN{5}CGC 32 9 3.61 409 68 GCCN{14}CGC 28 7 3.59 410 69 CAGN{11}CCC89 45 3.58 411 70 GGGN{16}GAC 53 21 3.57 412 71 CCCN{15}GCG 25 6 3.57413 72 CCCN{0}CGC 37 12 3.54 414 73 CCCN{16}AGC * 67 30 3.54 415 74AGGN{9}GGG 96 50 3.52 416 75 CGCN{12}CTC 28 7 3.46 417 76 CACN{8}CGC 235 3.43 418 77 CCAN{7}CCG 31 9 3.42 419 78 CGGN{1}GCA 25 6 3.41 420 79CGCN{14}CCC 29 8 3.4 421 80 AGCN{0}CCC 76 36 3.4 422 81 CGCN{13}GTC 18 33.37 423 82 GCGN{3}GCA 26 7 3.35 424 83 CGGN{0}GGC 34 11 3.35 425 84GCCN{14}CCC 68 31 3.33 426 85 ACCN{7}CGC 21 4 3.32 427 86 AGGN{7}CGG 3310 3.31 428 87 CCCN{16}CGA 22 5 3.3 429 88 CGCN{6}CAG 31 9 3.29 430 89CAGN{11}GCG 29 8 3.29 431 90 CCGN{12}CCG 19 4 3.26 432 91 CGCN{18}CAG 277 3.24 433 92 CAGN{1}GGG 80 39 3.21 434 93 CGCN{0}CCC 32 10 3.2 435 94GCGN{18}GCC 26 7 3.18 436 95 CGGN{15}GGC 27 7 3.15 437 96 CCCN{15}AGG 7234 3.14 438 97 AGGN{20}GCG 26 7 3.14 439 98 CGGN{5}CTC 26 7 3.13 440 99TCCN{17}CGA 23 5 3.12 441 100 GCGN{4}CCC 30 9 3.08 442 101 CCCN{2}CGC 309 3.07 443 102 CGTN{3}CAG 28 8 3.06 444 103 CCGN{13}GAG 27 7 3.05 445104 CTCN{6}CGC 28 8 3.04 446 105 CGCN{4}GAG 21 5 3.03 447 106 GCGN{5}GGA24 6 3.03 448 107 CCGN{1}CAG 27 7 3.01 449 108 CGCN{11}CCG 18 3 2.99 450109 GCGN{19}CCC 26 7 2.98 451 110 CGCN{18}GAA 21 5 2.98 452 111GGGN{19}GGA 78 39 2.95 453 112 CCAN{1}CGG 24 6 2.94 454 113 CCCN{7}GCG25 6 2.94 455 114 AGGN{10}CCC 84 43 2.92 456 115 CCAN{0}GGG 97 52 2.88457 116 CAGN{10}CCC 82 41 2.87 458 117 CCGN{18}CCG 19 4 2.86 459 118CCGN{18}GGC 26 7 2.85 460 119 CCCN{2}GCG 24 6 2.84 461 120 CGCN{1}GGC 257 2.83 462 121 CCGN{5}GAC 19 4 2.81 463 122 GGAN{0}CCC 52 22 2.8 464 123CCCN{1}CCG 29 9 2.78 465 124 CCCN{15}ACG 23 6 2.75 466 125 AGCN{8}CCC 6631 2.73 467 126 CCCN{3}GGC 60 27 2.71 468 127 AGGN{9}CGG 31 10 2.7 469128 CCCN{14}CGC 27 8 2.7 470 129 CCGN{0}CCG 19 4 2.7 471 130 CGCN{8}AGC23 6 2.69 472 131 CGCN{19}ACC 21 5 2.68 473 132 GCGN{17}GAC 17 3 2.66474 133 AGCN{1}GCG 24 6 2.63 475 134 CCGN{11}GGC 31 10 2.63 476 135CGGN{4}AGA 26 7 2.63 477 136 CGCN{14}CCG 17 3 2.62 478 137 CCTN{20}GCG24 6 2.62 479 138 CCAN{10}CGC 26 7 2.61 480 139 CCCN{20}CAC 69 33 2.6481 140 CCGN{11}GCC 27 8 2.6 482 141 CGCN{18}CCC 26 7 2.59 483 142CGGN{15}CGC 16 3 2.57 484 143 CGCN{16}GCC 24 6 2.55 485 144 CGCN{20}GGC23 6 2.54 486 145 CGCN{19}CCG 18 4 2.52 487 146 CGGN{10}CCA 28 8 2.51488 147 CGCN{17}CCC 26 7 2.51 489 148 CGCN{11}ACA 23 6 2.51 490 149CGGN{0}ACC 17 3 2.5 491 150 GCGN{10}GCC 24 6 2.49 492 151 GCGN{8}GAC 173 2.49 493 152 CCCN{15}GGG 84 32 2.44 494 153 CGGN{16}GGC 27 8 2.44 495154 CGCN{16}CCA 23 6 2.42 496 155 GCCN{3}CCC 73 36 2.4 497 156CAGN{4}GGG 94 51 2.4 498 157 CCCN{6}GCG 23 6 2.38 499 158 CCGN{16}CGC 173 2.38 500 159 CCCN{17}GCA 61 28 2.37 501 160 CGCN{13}TCC 24 6 2.37 502161 GCCN{1}CGC 29 9 2.36 503 162 CCGN{19}GAG 26 7 2.35 504 163GGGN{10}GGA 89 48 2.35 505 164 CAGN{5}CCG 32 11 2.35 506 165 CGCN{3}AGA19 4 2.32 507 166 GCCN{0}GCC 29 9 2.32 508 167 CCCN{8}GGC 61 28 2.31 509168 CCTN{6}GCG 22 6 2.29 510 169 GACN{6}CCC 48 20 2.29 511 170CGGN{1}CCC 26 8 2.27 512 171 CCCN{15}CCG 30 10 2.27 513 172 CAGN{9}CCC84 44 2.26 514 173 CGGN{10}GGC 27 8 2.26 515 174 CGAN{10}ACG 10 1 2.26516 175 GCGN{3}TCC 21 5 2.26 517 176 CCCN{3}GCC 75 38 2.24 518 177GCGN{1}ACC 17 3 2.24 519 178 CCGN{9}AGG 27 8 2.23 520 179 CGCN{16}CAG 268 2.23 521 180 GGCN{0}CCC 62 29 2.22 522 181 AGGN{12}CCG 26 8 2.19 523182 CCGN{0}GCG 16 3 2.19 524 183 CCGN{2}GCC 30 10 2.18 525 184CCGN{11}GTC 19 4 2.17 526 185 CAGN{0}CCC 88 47 2.17 527 186 CCCN{5}CCG32 11 2.17 528 187 GCCN{20}CCC 66 32 2.15 529 188 GACN{2}CGC 18 4 2.14530 189 CGCN{6}CAC 23 6 2.13 531 190 AGGN{14}GCG 25 7 2.1 532 191GACN{5}CGC 17 3 2.1 533 192 CCTN{19}CCG 29 9 2.1 534 193 CCGN{12}GGA 247 2.08 535 194 GGCN{9}GAC * 44 18 2.08 536 195 AGGN{10}GGG 94 52 2.07537 196 CCGN{10}GAG 25 7 2.07 538 197 CGCN{6}GGA 20 5 2.06 539 198CGCN{7}AGC 23 6 2.04 540 199 CCAN{13}CGG 26 8 2.03 541 200 CGGN{6}GGA 257 2.03 542 201 CGCN{19}GCC 24 7 2.03 543 202 CCAN{12}CGC 24 7 2.02 544203 CGGN{1}GGC 41 16 2.02 545 204 GCGN{3}CCA 25 7 2.01 546 205AGGN{1}CGC 21 5 2 547 206 CTCN{5}CGC 24 7 1.98 548 207 CCCN{0}ACG 30 101.97 549 208 CAGN{17}CCG 29 9 1.96 550 209 GGCN{4}CCC 62 30 1.96 551 210AGGN{8}GCG 26 8 1.96 552 211 CTGN{1}CCC 88 48 1.94 553 212 CCCN{16}CAG85 46 1.94 554 213 CGCN{9}GAC 16 3 1.93 555 214 CAGN{6}CCG 29 9 1.92 556215 CGTN{12}CGC 11 1 1.92 557 216 CTCN{7}GCC 69 35 1.92 558 217CGCN{19}TCC 22 6 1.92 559 218 CCCN{7}GCC 67 33 1.91 560 219 CAGN{13}CGG30 10 1.9 561 220 CGCN{1}GCC 27 8 1.9 562 221 CGCN{17}CCG 17 4 1.89 563222 AGGN{4}CCC 63 31 1.89 564 223 AGCN{10}CGC 21 5 1.89 565 224CCCN{11}CGG 30 10 1.88 566 225 CCCN{8}GCC 75 39 1.86 567 226 CCGN{1}CGG22 3 1.86 568 227 CCCN{1}ACC 71 36 1.85 569 228 CGCN{0}CAG 25 7 1.85 570229 CCGN{19}TGC 23 6 1.82 571 230 GCGN{4}CGA 12 2 1.82 572 231CCGN{19}GCC 30 10 1.82 573 232 CCAN{10}CCC 85 46 1.81 574 233CAGN{13}GGG 91 51 1.81 575 234 AGCN{18}CGG 23 6 1.81 576 235 CGAN{8}CGC11 1 1.81 577 236 AGCN{4}CCC 63 31 1.8 578 237 GGAN{6}CCC 61 30 1.8 579238 CGGN{13}AAG 23 6 1.8 580 239 ACCN{11}CGC 19 5 1.79 581 240CCGN{12}CAG 28 9 1.78 582 241 CCCN{12}GGG 76 29 1.77 583 242 CACN{17}ACG22 6 1.76 584 243 CAGN{18}CCC 82 44 1.76 585 244 CGTN{10}GTC 19 5 1.75586 245 CCCN{13}GCG 23 6 1.75 587 246 GCAN{1}CGC 20 5 1.73 588 247AGAN{4}CCG 24 7 1.73 589 248 GCGN{10}AGC 22 6 1.72 590 249 CGCN{0}GGA 122 1.72 591 250 CGGN{4}GAC 17 4 1.69 592 251 CCCN{12}CGC 26 8 1.68 593252 GCCN{15}CCC 65 33 1.68 594 253 GCGN{6}TCC 20 5 1.66 595 254CGGN{3}CAG 33 12 1.65 596 255 CCCN{3}CCA 88 49 1.65 597 256 AGCN{3}CCC59 28 1.65 598 257 GGGN{16}GCA 65 33 1.65 599 258 AGGN{8}CCG 28 9 1.64600 259 CCCN{0}CCG 29 10 1.64 601 260 GCGN{5}GAC 16 3 1.64 602 261CCCN{9}ACC 60 29 1.64 603 262 CTGN{5}CGC 25 8 1.64 604 263 CGCN{14}CTC23 7 1.64 605 264 CGGN{14}GCA 23 7 1.63 606 265 CCGN{8}GCC 26 8 1.62 607266 CCGN{7}CAC 23 7 1.62 608 267 AGCN{8}GCG 21 6 1.61 609 268CGGN{16}GGA 29 10 1.61 610 269 CCAN{12}CCG 26 8 1.61 611 270 CGGN{2}CCC26 8 1.6 612 271 CCAN{13}GGG 71 37 1.6 613 272 CGGN{15}GCA 21 6 1.6 614273 CGCN{9}GCA 20 5 1.58 615 274 CGGN{19}CCA 26 8 1.58 616 275GGGN{15}CGA 20 5 1.57 617 276 CCCN{10}CGC 26 8 1.57 618 277 CTCN{14}CGC26 8 1.55 619 278 CACN{11}GCG 20 5 1.55 620 279 CCGN{2}GGC 24 7 1.55 621280 CTGN{18}CCC 85 47 1.54 622 281 GGGN{13}CAC 58 28 1.54 623 282CCTN{15}GGC 62 31 1.54 624 283 CCCN{20}CGA 20 5 1.54 625 284 CCCN{8}CGA20 5 1.53 626 285 GAGN{7}CCC 61 30 1.53 627 286 CGCN{2}CCG 22 6 1.53 628287 CCCN{0}TCC 98 57 1.52 629 288 AGCN{0}GCC 21 6 1.52 630 289CCCN{2}TCC 82 45 1.52 631 290 CCGN{5}CCC 30 10 1.52 632 291 CGCN{13}CGC16 3 1.51 633 292 CCCN{1}CGC 28 9 1.51 634 293 GCCN{16}GCA 53 25 1.51635 294 CCCN{16}CCA 84 46 1.5 636 295 CCGN{13}CGC 19 5 1.5 637 296CCGN{17}CAG 28 9 1.49 638 297 CGGN{18}GGC 26 8 1.49 639 298 CCGN{14}AGG23 7 1.49 640 299 CCCN{5}CGG 26 8 1.49 641 300 CCCN{6}GGA 58 28 1.49 642301 ACGN{2}CCC 20 5 1.49 643 302 CCAN{9}CCG 27 9 1.48 644 303CCCN{19}CCA 78 42 1.48 645 304 CAGN{0}GGG 77 41 1.48 646 305 AGCN{1}CCC58 28 1.47 647 306 GCGN{7}TCC 27 9 1.46 648 307 ACGN{18}CCA 25 8 1.46649 308 GCTN{14}CCC 61 30 1.46 650 309 GCGN{14}CCC 23 7 1.46 651 310GCGN{19}AGC 20 5 1.45 652 311 CCGN{8}CAG 29 10 1.45 653 312 GCGN{6}GCC22 6 1.45 654 313 GCGN{10}GCA 20 5 1.44 655 314 CCTN{7}GCC 69 36 1.44656 315 GCCN{13}GCC 54 26 1.42 657 316 CCCN{14}GCC 63 32 1.42 658 317CCCN{15}CGG 26 8 1.42 659 318 CCAN{13}CGC 23 7 1.42 660 319 AGCN{11}GGG67 35 1.41 661 320 GGAN{0}GCC 64 32 1.4 662 321 GCCN{3}TCC 61 30 1.4 663322 CCTN{5}GCC 69 36 1.39 664 323 CGGN{18}CCC 25 8 1.39 665 324CCTN{3}GGC 59 29 1.38 666 325 CCGN{0}CTC 22 6 1.38 667 326 AGCN{17}GCG19 5 1.37 668 327 ACGN{14}GGG 20 5 1.37 669 328 CGAN{12}GGC 19 5 1.37670 329 CCCN{20}CGC 24 7 1.37 671 330 ACGN{12}CTG 24 7 1.36 672 331CCGN{0}CCC 36 14 1.36 673 332 CCGN{10}GGA 23 7 1.36 674 333 CCCN{3}GCG21 6 1.36 675 334 GCGN{14}CGC 22 3 1.35 676 335 CCGN{8}CGC 16 4 1.35 677336 CGCN{10}ACA 22 6 1.34 678 337 CCCN{19}CCG 28 10 1.33 679 338CACN{14}CGC 20 5 1.32 680 339 GACN{3}GGC 46 21 1.32 681 340 GAAN{7}CGC19 5 1.32 682 341 CGCN{16}GGC 21 6 1.31 683 342 GGCN{9}CCC 64 33 1.31684 343 CCCN{9}GCC 64 33 1.31 685 344 CGCN{0}TGC 26 9 1.3 686 345CCTN{8}GGC 67 35 1.3 687 346 CCAN{8}CCC 82 46 1.29 688 347 GACN{2}CCC 4218 1.28 689 348 GGCN{1}CCC 54 26 1.27 690 349 CGCN{0}AGC 24 7 1.26 691350 AGGN{4}GCG 28 10 1.26 692 351 CGGN{6}TCC 22 6 1.25 693 352ACGN{19}GGC 20 5 1.25 694 353 CCCN{8}ACG 21 6 1.24 695 354 CCCN{18}GCC62 31 1.24 696 355 GCCN{2}CGA 19 5 1.24 697 356 CCCN{8}GCG 28 10 1.23698 357 CCCN{0}CTC 76 41 1.23 699 358 GCCN{11}CGC 27 9 1.22 700 359AGCN{9}CCC 59 29 1.22 701 360 GCTN{0}GCC 71 38 1.21 702 361 CGCN{3}CCC26 9 1.21 703 362 CCCN{2}CCC 117 72 1.19 704 363 GCCN{9}CGC 23 7 1.19705 364 GCAN{19}CGC 19 5 1.19 706 365 CAGN{4}CGG 32 12 1.18 707 366CAGN{2}GGG 80 44 1.17 708 367 GCCN{16}CCC 67 35 1.16 709 368 GAGN{5}CCC60 30 1.16 710 369 CCTN{16}TCG 20 6 1.16 711 370 CCCN{2}GGC 62 32 1.15712 371 GCGN{13}GGA 24 8 1.15 713 372 GCCN{17}GGC 66 25 1.15 714 373CCCN{14}GGC 58 29 1.14 715 374 AGGN{3}CCG 31 12 1.14 716 375 CACN{0}CGC32 12 1.14 717 376 CGGN{18}CAG 28 10 1.14 718 377 AGCN{1}GCC 57 28 1.13719 378 CGCN{18}GGC 23 7 1.13 720 379 CCCN{5}AGG 64 33 1.11 721 380AACN{0}GCG 9 1 1.11 722 381 CCCN{10}CCA 88 50 1.09 723 382 CGCN{13}GAG20 6 1.09 724 383 CGCN{7}GCC 25 8 1.08 725 384 CCCN{9}CCG 28 10 1.07 726385 CGCN{16}CCC 24 8 1.05 727 386 GAAN{13}CGC 18 5 1.05 728 387GGCN{3}CCC 49 23 1.03 729 388 TCCN{11}CCA 87 50 1.03 730 389 CACN{0}CCC70 38 1.02 731 390 CGCN{16}CCG 15 3 1.02 732 391 CGGN{15}AGC 21 6 1.02733 392 CCCN{12}GCG 21 6 1.02 734 393 CCCN{9}GAG 59 30 1.01 735 394CCGN{20}TCC 24 8 1.01 736 395 CGCN{0}CGC 17 4 1.01 737 396 ATGN{7}CGG 206 1 738 397 GGGN{20}GCA 59 30 1 739 398 CGGN{4}GGC 26 9 0.99 740 399CGGN{16}AGC 22 7 0.99 741 400 CGGN{5}GGC 25 8 0.99 742 401 GCGN{0}GGA 258 0.98 743 402 GGCN{20}CAC 52 25 0.98 744 403 CCCN{9}CCC 97 58 0.97 745404 ACCN{17}GGC 44 20 0.97 746 405 CCCN{6}CGA 18 5 0.96 747 406AAGN{10}CGG 26 9 0.96 748 407 CGCN{17}CAC 21 6 0.95 749 408 CCCN{16}CGG25 8 0.94 750 409 GACN{18}GGC 39 17 0.94 751 410 GGGN{15}GAC 47 22 0.92752 411 GCCN{4}TCC 66 35 0.92 753 412 GGCN{15}CCC 56 28 0.92 754 413CAGN{12}CGC 24 8 0.92 755 414 CCAN{3}GCG 22 7 0.91 756 415 CCGN{16}GAG22 7 0.9 757 416 AGCN{2}CGC 24 8 0.89 758 417 GAGN{4}CCC 54 27 0.89 759418 AGGN{3}CGC 23 7 0.88 760 419 CACN{13}AGG * 67 36 0.88 761 420CCCN{4}CAG 88 51 0.88 762 421 CCCN{2}GAA 63 33 0.87 763 422 CGCN{19}GAG21 6 0.87 764 423 ACGN{18}GGG 21 6 0.87 765 424 CCCN{4}GGC 62 32 0.87766 425 CGGN{9}GAG 28 10 0.86 767 426 CCCN{3}GGG 66 26 0.86 768 427GAGN{4}GGC 66 35 0.85 769 428 CGCN{5}GAG 18 5 0.84 770 429 CCGN{20}AGG24 8 0.84 771 430 CCCN{15}CCC 88 51 0.83 772 431 AGGN{17}CCG 25 8 0.82773 432 AGGN{6}GGG 89 52 0.82 774 433 GGCN{20}CCC 57 29 0.82 775 434GCAN{17}CGC 19 5 0.82 776 435 CGAN{11}ACG 9 1 0.81 777 436 CGCN{2}GGA 195 0.81 778 437 CTGN{5}CCC 79 45 0.8 779 438 TCCN{20}CCA 77 43 0.8 780439 CCAN{2}GGG 59 30 0.8 781 440 CCGN{15}GCG 14 3 0.8 782 441 CCAN{5}GGG69 38 0.79 783 442 CGGN{1}TGC 24 8 0.79 784 443 CCCN{14}GCG 21 6 0.79785 444 CAGN{0}CCG 27 10 0.79 786 445 GCCN{9}TCC 60 31 0.78 787 446AGGN{20}CGC 22 7 0.78 788 447 CCCN{6}GAC 42 19 0.77 789 448 CGGN{11}CCA23 7 0.76 790 449 GGGN{14}CAC 57 29 0.75 791 450 GCAN{15}CGC 19 5 0.74792 451 CGCN{2}ACA 20 6 0.74 793 452 ACCN{9}CCC 57 29 0.73 794 453GCGN{9}CGC 20 3 0.73 795 454 CAGN{15}GCG 23 7 0.73 796 455 CCCN{18}GTC45 21 0.72 797 456 GCGN{3}CCC 24 8 0.72 798 457 CGGN{11}GCC 23 8 0.72799 458 CCCN{1}CGG 24 8 0.71 800 459 GCCN{4}CCA 70 38 0.71 801 460CCCN{4}CCG 30 12 0.7 802 461 CGTN{2}GCA 21 6 0.7 803 462 AGCN{7}TCG 18 50.69 804 463 CCGN{15}GAA 20 6 0.69 805 464 ACCN{5}CCC 62 33 0.69 806 465CGCN{14}GAG 19 5 0.68 807 466 CCCN{7}CGC 30 12 0.68 808 467 GAGN{12}CGC21 6 0.68 809 468 GGCN{17}CCC 58 30 0.67 810 469 ACGN{11}CTC 21 7 0.65811 470 ACAN{9}CGG 24 8 0.65 812 471 CTGN{7}CCC 82 47 0.65 813 472CCCN{2}GCC 72 40 0.65 814 473 CGGN{2}GCA 24 8 0.64 815 474 CCCN{0}TGC 8348 0.64 816 475 CGCN{7}ACC 18 5 0.63 817 476 GCAN{2}GCC 54 27 0.63 818477 GCGN{8}CCA 20 6 0.63 819 478 AGCN{0}CGC 22 7 0.63 820 479 GCGN{2}GCA18 5 0.63 821 480 CCGN{2}GTC 18 5 0.62 822 481 CCGN{3}ACA 21 7 0.62 823482 ACGN{13}TGG 21 7 0.62 824 483 CCAN{8}CGC 23 8 0.62 825 484CCGN{9}GGC 23 8 0.61 826 485 CCAN{5}CCG 25 9 0.61 827 486 AGGN{3}GGG 9759 0.61 828 487 CAGN{2}GGC 78 45 0.61 829 488 CCCN{8}CAG 81 47 0.61 830489 AGCN{5}CAG 80 46 0.6 831 490 CGGN{16}GCC 22 7 0.6 832 491GCGN{15}CCC 23 8 0.6 833 492 CCCN{11}GCC 59 31 0.59 834 493 CGAN{2}ACG 91 0.59 835 494 CGGN{4}GCC 22 7 0.59 836 495 CACN{6}CGC 19 6 0.59 837 496CGGN{5}ACG 11 2 0.59 838 497 CTGN{4}GCC * 66 36 0.59 839 498 GGGN{18}CGA18 5 0.59 840 499 CCTN{8}CGC 22 7 0.59 841 500 GCCN{4}CCC 67 37 0.58 842501 CGGN{10}GCC 22 7 0.58 843 502 GCCN{5}GGA 54 27 0.57 844 503ACCN{7}GCG 15 4 0.57 845 504 CCCN{8}CGC 24 8 0.57 846 505 CAGN{5}CCC 7744 0.56 847 506 CACN{14}GGA 63 34 0.56 848 507 CCCN{1}GCC 94 57 0.55 849508 CCCN{5}AGC 67 37 0.55 850 509 GGCN{5}GGA 59 31 0.55 851 510CGAN{17}GAG 19 6 0.55 852 511 CGCN{7}ACA 18 5 0.54 853 512 CCAN{13}CCC87 52 0.54 854 513 CGGN{20}GGC 24 8 0.54 855 514 CCCN{17}GCC 58 30 0.53856 515 CCTN{10}CCG 30 12 0.53 857 516 CCCN{8}CCG 27 10 0.53 858 517CGCN{3}GAG 18 5 0.52 859 518 CGCN{7}AAG 17 5 0.51 860 519 CGGN{11}GGA 238 0.51 861 520 CCGN{15}CCG 15 4 0.51 862 521 CCCN{3}GCA 57 30 0.51 863522 CGGN{2}CAG 24 8 0.5 864 523 AGGN{2}CCG 24 8 0.5 865 524 CCCN{4}CAC69 38 0.5 866 525 GGAN{19}CCC 56 29 0.49 867 526 CCCN{8}CAC 68 38 0.49868 527 ACCN{6}CCG 18 5 0.49 869 528 CCCN{6}GGC 54 28 0.49 870 529CCCN{6}CCG 29 11 0.48 871 530 CGCN{14}GCC 26 9 0.47 872 531 CCGN{5}TCC25 9 0.46 873 532 GCCN{6}GCC 55 28 0.46 874 533 CGGN{7}GGA 24 8 0.45 875534 GGGN{6}GGA 87 52 0.44 876 535 GCCN{12}TCC 60 32 0.44 877 536AGTN{16}CCG 17 5 0.44 878 537 GGCN{19}GCC 68 29 0.44 879 538 CCGN{3}CCG22 7 0.44 880 539 CCCN{8}ACC 58 31 0.44 881 540 CAGN{15}GCC 77 44 0.44882 541 CCCN{17}CGG 24 8 0.44 883 542 GCGN{1}CCA 22 7 0.44 884 543CCCN{14}CAG 79 46 0.44 885 544 CCCN{8}CCC 89 53 0.44 886 545 ACAN{12}GCG23 8 0.43 887 546 AGGN{4}CCG 23 8 0.43 888 547 CGCN{13}GCC 23 8 0.43 889548 GAGN{2}CGC 23 8 0.42 890 549 CCCN{9}GCG 21 7 0.42 891 550CGCN{17}ACA 17 5 0.42 892 551 GCGN{17}CCA 23 8 0.42 893 552 AAGN{18}CCG20 6 0.42 894 553 CGCN{1}GGA 18 5 0.41 895 554 CCAN{1}CCC 90 54 0.41 896555 CGTN{18}TGC 20 6 0.41 897 556 TCCN{14}CGA 17 5 0.41 898 557CACN{5}GGG 56 29 0.4 899 558 CCGN{12}GCA 21 7 0.4 900 559 CTGN{6}CCC 7744 0.4 901 560 CGGN{8}GGC 32 13 0.4 902 561 CCAN{11}GGG 68 38 0.4 903562 ACGN{19}CAA 21 7 0.39 904 563 GGGN{20}CCC 72 31 0.39 905 564CGCN{3}CAG 23 8 0.39 906 565 AGCN{17}GGG 58 31 0.37 907 566 CACN{20}CCG21 7 0.37 908 567 ACGN{17}CAG 24 8 0.37 909 568 AGGN{1}CCC 60 32 0.37910 569 CGTN{12}CAC 20 6 0.37 911 570 CGGN{9}GGC 23 8 0.37 912 571CGCN{10}GCG 18 3 0.37 913 572 CCCN{6}CTC 80 47 0.36 914 573 CCGN{10}AGG23 8 0.36 915 574 CCCN{18}CAG 79 46 0.36 916 575 AGCN{17}CCG 21 7 0.36917 576 AGCN{9}GCG 18 5 0.36 918 577 CCAN{3}GGC 62 34 0.36 919 578CCCN{11}GGC 57 30 0.35 920 579 ACGN{5}GCA 23 8 0.35 921 580 CCCN{14}CGG23 8 0.35 922 581 CCCN{5}CCA 91 55 0.35 923 582 CCGN{1}AGG 22 7 0.34 924583 GGGN{10}GAC 45 22 0.34 925 584 CGCN{15}CCA 20 6 0.34 926 585CCTN{19}CGC 22 7 0.34 927 586 CGTN{3}CGC 10 2 0.33 928 587 AGCN{14}CCG21 7 0.33 929 588 GGCN{2}CGA 17 5 0.33 930 589 CAGN{8}CCC 79 46 0.33 931590 CCGN{2}GAC 16 4 0.33 932 591 AGCN{19}AGG 70 40 0.32 933 592CCTN{4}GGC 64 35 0.32 934 593 CCGN{11}AGC 22 7 0.32 935 594 CACN{4}CGC18 5 0.32 936 595 CCGN{1}CCC 30 12 0.31 937 596 CTGN{13}GGC 73 42 0.31938 597 CGCN{16}ACC 15 4 0.31 939 598 CACN{18}CAG 79 46 0.31 940 599GGCN{8}GCC 68 29 0.29 941 600 GGGN{15}GGA 78 46 0.29 942 601 CCGN{16}GCC22 7 0.29 943 602 CCGN{20}ACC 18 5 0.29 944 603 CGAN{7}CCC 17 5 0.28 945604 CCGN{6}CTC 23 8 0.28 946 605 CGGN{10}CTC 22 7 0.28 947 606CAGN{16}CGC 23 8 0.28 948 607 CCAN{3}AGG 77 45 0.27 949 608 GCCN{18}GCC52 27 0.27 950 609 CGCN{18}GGA 19 6 0.26 951 610 CCGN{20}GGC 22 7 0.26952 611 ACAN{10}GCG 17 5 0.26 953 612 CGGN{5}CCC 25 9 0.25 954 613CCCN{7}TCC 75 43 0.25 955 614 ACGN{10}CGC 10 2 0.25 956 615 CCCN{3}TCC81 48 0.25 957 616 CCGN{8}CGG 20 3 0.24 958 617 CCAN{15}CGG 22 7 0.24959 618 CCGN{6}CCG 17 5 0.24 960 619 CAGN{3}GCG 25 9 0.24 961 620GAGN{1}CCC 62 34 0.24 962 621 CCGN{18}TGC 22 7 0.23 963 622 CCCN{7}CCA85 51 0.23 964 623 CGGN{3}CCA 24 9 0.23 965 624 ACGN{1}CCC 18 5 0.23 966625 CGGN{13}TGA 21 7 0.22 967 626 CTCN{6}GGC 53 28 0.22 968 627GCGN{2}GAC 15 4 0.22 969 628 GGGN{11}ACC 49 25 0.22 970 629 CGCN{4}GGA17 5 0.22 971 630 CCCN{11}CCG 27 10 0.22 972 631 CCGN{19}GCA 20 6 0.22973 632 GCGN{0}GCA 20 6 0.21 974 633 AGAN{7}CCC 61 33 0.21 975 634CGGN{2}CCA 21 7 0.21 976 635 CCCN{7}CCC 89 54 0.21 977 636 ACCN{4}GCG 154 0.2 978 637 CCTN{15}CGC 20 6 0.2 979 638 AGCN{9}GTC 44 21 0.2 980 639CCCN{18}CTC 74 43 0.2 981 640 CGCN{18}CGA 9 1 0.19 982 641 CCCN{15}GCC62 34 0.18 983 642 ACCN{11}GGC 45 22 0.18 984 643 AGGN{15}CGC 29 12 0.18985 644 GCGN{0}CCA 27 10 0.18 986 645 GCGN{9}AGC 18 5 0.17 987 646GGGN{18}GCA 59 32 0.17 988 647 CCCN{17}CAG 77 45 0.17 989 648 CCAN{8}CGG22 8 0.16 990 649 CCGN{10}GGC 21 7 0.16 991 650 GCAN{0}GCC 76 44 0.16992 651 CAGN{2}CGC 20 6 0.16 993 652 CGCN{8}GGC 19 6 0.16 994 653CTGN{17}GGC 65 36 0.16 995 654 GGGN{14}ACC 46 23 0.16 996 655 CCGN{1}TGC20 6 0.16 997 656 CAGN{8}CGC 22 8 0.15 998 657 AAGN{11}CGC 17 5 0.15 999658 CCGN{6}TCC 22 8 0.14 1000 659 CCAN{18}CCC 72 42 0.14 1001 660CCAN{0}CCC 84 51 0.14 1002 661 GAGN{6}CCC 53 28 0.14 1003 662AGCN{20}GGC 52 27 0.14 1004 663 CAGN{0}CGC 21 7 0.14 1005 664CCGN{12}CTC 22 8 0.14 1006 665 CGCN{15}ACG 9 1 0.13 1007 666 GGCN{17}CGA15 4 0.13 1008 667 CCGN{16}AAG 19 6 0.13 1009 668 CGCN{14}TCC 19 6 0.121010 669 AGGN{7}CGC 20 7 0.12 1011 670 CGGN{7}CCC 22 8 0.12 1012 671CGCN{4}GCC 34 15 0.12 1013 672 CGAN{6}CCC 17 5 0.12 1014 673 CCCN{19}GGA60 33 0.11 1015 674 CCCN{16}GCG 28 11 0.11 1016 675 CCAN{7}CGC 20 7 0.111017 676 CCCN{6}GCC 80 48 0.11 1018 677 GCCN{14}TCC 55 29 0.11 1019 678AGGN{14}GCC 64 36 0.1 1020 679 CGCN{11}GCC 20 7 0.1 1021 680 TCCN{0}GCA17 5 0.09 1022 681 GCGN{8}CCC 27 11 0.09 1023 682 CCAN{11}GCG 19 6 0.091024 683 CACN{4}GGG 51 26 0.09 1025 684 CGGN{7}TCC 20 7 0.09 1026 685GCGN{5}GCC 20 7 0.09 1027 686 ACGN{12}CAG 26 10 0.09 1028 687CCGN{19}CGC 14 4 0.08 1029 688 CGGN{8}TGC 18 5 0.08 1030 689 CCCN{1}GAG65 37 0.07 1031 690 GCGN{19}TGA 18 6 0.07 1032 691 GGCN{15}GCC 70 310.07 1033 692 CCGN{7}CCC 27 11 0.07 1034 693 ACAN{19}CCC 63 35 0.07 1035694 ACCN{16}GGG 47 24 0.07 1036 695 AGAN{1}GGC 64 36 0.07 1037 696GGGN{17}TGA 64 36 0.06 1038 697 CAGN{5}GGG 83 50 0.06 1039 698GCCN{13}CGC 22 8 0.06 1040 699 GCGN{7}GGA 19 6 0.06 1041 700 CAGN{14}CCA94 58 0.06 1042 701 CCGN{4}GTC 16 4 0.06 1043 702 CCCN{13}CGC 22 8 0.061044 703 GCGN{14}ACC 15 4 0.05 1045 704 CAGN{20}GGG 81 49 0.05 1046 705CCGN{4}CCC 27 11 0.05 1047 706 CGCN{5}GGC 18 6 0.05 1048 707 CCTN{6}GGC57 31 0.05 1049 708 AGGN{3}GGC 67 38 0.05 1050 709 CGGN{11}CGC 14 4 0.051051 710 CTGN{18}GGA 77 46 0.04 1052 711 CACN{17}CCA 74 43 0.04 1053 712CGGN{3}GAG 22 8 0.04 1054 713 CCCN{9}CCA 82 49 0.03 1055 714 CCCN{1}ACG18 6 0.03 1056 715 CAGN{1}GCC 72 42 0.03 1057 716 AGGN{6}CCG 23 8 0.031058 717 AGCN{9}GGG 57 31 0.03 1059 718 CCCN{7}GGC 54 29 0.02 1060 719CCTN{13}CCC 88 54 0.02 1061 720 CCGN{19}TTC 20 7 0.02 1062 721CCCN{7}CCG 27 11 0.02 1063 722 CGAN{6}GGC 17 5 0.01 1064 723 CGGN{4}CTC21 7 0.01 1065 724 CGGN{0}CGC 13 3 0.01 1066 725 CCTN{13}ACG 19 6 0.011067 726 GGGN{6}CAC 53 28 0.01 1068 727 CCCN{16}CGC 21 7 0.01 1069 728CCCN{10}CTC 76 45 0 1070 729 CCCN{0}CAG 92 57 0 1071 730 GCCN{5}CCC 6537 0 1072

TABLE 8 Candidate STAR elements tested by Linear Discriminant Analysis(SEQ ID NOS: 66-84) SEQ ID NO: Candidate STAR Location¹ Length 66 T2 F20q13.33 ~2800 67 T2 R 6q14.1 ~2800 68 T3 F 15q12 ~2900 69 T3 R 7q31.2~2900 70 T5 F 9q34.13 ND² 71 T5 R 9q34.13 ND 72 T7 22q12.3 ~1200 73 T9 F21q22.2 ~1600 74 T9 R 22q11.22 ~1600 75 T10 F 7q22.2 ~1300 76 T10 R6q14.1 ~1300 77 T11 F 17q23.3 ~2000 78 T11 R 16q23.1 ~2000 79 T12 4p15.1~2100 80 T13 F 20p13 ~1700 81 T13 R 1p13.3 ~1700 82 T14 R 11q25 ~1500 83T17 2q31.3 ND 84 T18 2q31.1 ND ¹Chromosomal location is determined byBLAT search of DNA sequence data from the STAR elements against thehuman genome database. The location is given according to standardnomenclature referring to the cytogenetic ideogram of each chromosome;e.g., 1p2.3 is the third cytogenetic sub-band of the second cytogeneticband of the short arm of chromosome 1(http://www.ncbi.nlm.nih.gov/Class/MLACourse/Genetics/chrombanding.html).F, forward sequencing reaction result; R, reverse sequencing reactionresult. When the forward and reverse sequencing results mapped todifferent genomic locations, each sequence was extended to the fulllength of the original clone (as determined by restriction mapping)based on sequence information from the human genome database. ²ND: NotDetermined.

TABLE 9 Arabidopsis STAR elements of the invention, including chromosomelocation and length (SEQ ID NOS: 85-119) STAR Chromosome Length, kb SEQID NO: A1 I 1.2 85 A2 I 0.9 86 A3 I 0.9 87 A4 I 0.8 88 A5 I 1.3 89 A6 I1.4 90 A7 II 1.2 91 A8 II 0.8 92 A9 II 0.9 93 A10 II 1.7 94 A11 II 1.995 A12 II 1.4 96 A13 II 1.2 97 A14 II 2.1 98 A15 II 1.4 99 A16 II 0.7100 A17 II 1.5 101 A18 III 1.5 102 A19 III 0.7 103 A20 III 2.0 104 A21IV 1.8 105 A22 IV 0.8 106 A23 IV 0.6 107 A24 IV 0.5 108 A25 V 0.9 109A26 V 1.9 110 A27 V 1.1 111 A28 V 1.6 112 A29 V 0.9 113 A30 V 2.0 114A31 V 2.0 115 A32 V 1.3 116 A33 V 0.9 117 A34 I 0.9 118 A35 II 1.1 119

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1. A method for producing a proteinaceous molecule in a cell comprising:providing a cell selected from the group consisting of: a cell having anadenovirus Early Region 1 (E1) sequence, a HuNS-1 myeloma cell, a 293cell, a CHO cell, a Vero cell, a WERI-Rb-1 retinoblastoma cell, a BHKcell, a non-secreting mouse myeloma Sp2/0-Ag 14 cell, a non-secretingmouse myeloma NSO cell, and an NCI-H295R adrenal gland carcinoma cell;wherein said cell comprises an anti-repressor activity sequence operablylinked to a nucleic acid sequence encoding a heterologous proteinaceousmolecule, wherein said anti-repressor activity sequence comprises SEQ IDNO:44; expressing the proteinaceous molecule in said cell; and isolatingsaid proteinaceous molecule.
 2. The method of claim 1, wherein saidanti-repressor activity sequence is SEQ ID NO:44.
 3. The method of claim1, wherein said cell comprises an adenovirus Early Region 1 (E1)sequence.
 4. The method of claim 1, wherein said proteinaceous moleculeis secreted by said cell.
 5. The method of claim 2, wherein saidproteinaceous molecule is secreted by said cell.
 6. The method of claim1, wherein said cell comprises a plurality of the anti-repressoractivity sequence operably linked to said nucleic acid sequence encodingthe heterologous proteinaceous molecule.
 7. The method of claim 6,wherein at least one anti-repressor activity sequence is positioned 5′of the sequence encoding the proteinaceous molecule and at least oneanti-repressor activity sequence is positioned 3′ of the sequenceencoding the proteinaceous molecule.
 8. The method of claim 1, whereinsaid cell is a CHO cell.
 9. The method of claim 6, wherein said cell isa CHO cell.
 10. The method of claim 7, wherein said cell is a CHO cell.11. A recombinant host cell line, comprising: a cell selected from thegroup consisting of: a cell line comprising an adenovirus Early Region 1(E1) sequence, a HuNS-1 myeloma cell line, a 293 cell line, a CHO cellline, a Vero cell line, a WERI-Rb-1 retinoblastoma cell line, a BHK cellline, a non-secreting mouse myeloma Sp2/0-Ag 14 cell line, anon-secreting mouse myeloma NSO cell line, and an NCI-H295R adrenalgland carcinoma cell line; said cell comprising an anti-repressoractivity sequence operably linked to a nucleic acid sequence encoding aheterologous proteinaceous molecule, wherein said anti-repressoractivity sequence comprises SEQ ID NO:44.
 12. The cell line of claim 11,wherein said anti-repressor activity sequence is SEQ ID NO:44.
 13. Thecell line of claim 11, wherein said cell line comprises an adenovirusEarly Region 1 sequence.
 14. The cell line of claim 11, wherein saidcell comprises a plurality of the anti-repressor activity sequenceoperably linked to said nucleic acid sequence encoding the heterologousproteinaceous molecule.
 15. The cell line of claim 11, wherein at leastone anti-repressor activity sequence is positioned 5′ of the sequenceencoding the proteinaceous molecule and at least one anti-repressoractivity sequence is positioned 3′ of the sequence encoding theproteinaceous molecule.
 16. The cell line of claim 11, wherein said cellline is a CHO cell line.
 17. The cell line of claim 14, wherein saidcell line is a CHO cell line.
 18. The cell line of claim 15, whereinsaid cell line is a CHO cell line.